RLumShiny/0000755000176200001440000000000012743716614012157 5ustar liggesusersRLumShiny/inst/0000755000176200001440000000000012743662035013131 5ustar liggesusersRLumShiny/inst/www/0000755000176200001440000000000012743662035013755 5ustar liggesusersRLumShiny/inst/www/jscolor_inputBinding.js0000644000176200001440000000070512743662035020502 0ustar liggesusers// JSColor shiny input binding var jscolor = new Shiny.InputBinding(); $.extend(jscolor, { find: function(scope) { return $(scope).find("input.color"); }, getValue: function(el) { return $(el).val() }, subscribe: function(el, callback) { $(el).on("afterChange", function(e) { callback(); }); }, unsubscribe: function(el) { $(el).off("input.color"); } }); Shiny.inputBindings.register(jscolor);RLumShiny/inst/www/jscolor/0000755000176200001440000000000012743662035015430 5ustar liggesusersRLumShiny/inst/www/jscolor/demo.html0000644000176200001440000000027212743662035017243 0ustar liggesusers jscolor demo Click here: RLumShiny/inst/www/jscolor/arrow.gif0000644000176200001440000000010212743662035017242 0ustar liggesusersGIF89a  preloading : true, // use image preloading? install : function() { jscolor.addEvent(window, 'load', jscolor.init); }, init : function() { if(jscolor.binding) { jscolor.bind(); } if(jscolor.preloading) { jscolor.preload(); } }, getDir : function() { if(!jscolor.dir) { var detected = jscolor.detectDir(); jscolor.dir = detected!==false ? detected : 'jscolor/'; } return jscolor.dir; }, detectDir : function() { var base = location.href; var e = document.getElementsByTagName('base'); for(var i=0; i vs[a] ? (-vp[a]+tp[a]+ts[a]/2 > vs[a]/2 && tp[a]+ts[a]-ps[a] >= 0 ? tp[a]+ts[a]-ps[a] : tp[a]) : tp[a], -vp[b]+tp[b]+ts[b]+ps[b]-l+l*c > vs[b] ? (-vp[b]+tp[b]+ts[b]/2 > vs[b]/2 && tp[b]+ts[b]-l-l*c >= 0 ? tp[b]+ts[b]-l-l*c : tp[b]+ts[b]-l+l*c) : (tp[b]+ts[b]-l+l*c >= 0 ? tp[b]+ts[b]-l+l*c : tp[b]+ts[b]-l-l*c) ]; } drawPicker(pp[a], pp[b]); } }; this.importColor = function() { if(!valueElement) { this.exportColor(); } else { if(!this.adjust) { if(!this.fromString(valueElement.value, leaveValue)) { styleElement.style.backgroundImage = styleElement.jscStyle.backgroundImage; styleElement.style.backgroundColor = styleElement.jscStyle.backgroundColor; styleElement.style.color = styleElement.jscStyle.color; this.exportColor(leaveValue | leaveStyle); } } else if(!this.required && /^\s*$/.test(valueElement.value)) { valueElement.value = ''; styleElement.style.backgroundImage = styleElement.jscStyle.backgroundImage; styleElement.style.backgroundColor = styleElement.jscStyle.backgroundColor; styleElement.style.color = styleElement.jscStyle.color; this.exportColor(leaveValue | leaveStyle); } else if(this.fromString(valueElement.value)) { // OK } else { this.exportColor(); } } }; this.exportColor = function(flags) { if(!(flags & leaveValue) && valueElement) { var value = this.toString(); if(this.caps) { value = value.toUpperCase(); } if(this.hash) { value = '#'+value; } valueElement.value = value; } if(!(flags & leaveStyle) && styleElement) { styleElement.style.backgroundImage = "none"; styleElement.style.backgroundColor = '#'+this.toString(); styleElement.style.color = 0.213 * this.rgb[0] + 0.715 * this.rgb[1] + 0.072 * this.rgb[2] < 0.5 ? '#FFF' : '#000'; } if(!(flags & leavePad) && isPickerOwner()) { redrawPad(); } if(!(flags & leaveSld) && isPickerOwner()) { redrawSld(); } }; this.fromHSV = function(h, s, v, flags) { // null = don't change if(h !== null) { h = Math.max(0.0, this.minH, Math.min(6.0, this.maxH, h)); } if(s !== null) { s = Math.max(0.0, this.minS, Math.min(1.0, this.maxS, s)); } if(v !== null) { v = Math.max(0.0, this.minV, Math.min(1.0, this.maxV, v)); } this.rgb = HSV_RGB( h===null ? this.hsv[0] : (this.hsv[0]=h), s===null ? this.hsv[1] : (this.hsv[1]=s), v===null ? this.hsv[2] : (this.hsv[2]=v) ); this.exportColor(flags); }; this.fromRGB = function(r, g, b, flags) { // null = don't change if(r !== null) { r = Math.max(0.0, Math.min(1.0, r)); } if(g !== null) { g = Math.max(0.0, Math.min(1.0, g)); } if(b !== null) { b = Math.max(0.0, Math.min(1.0, b)); } var hsv = RGB_HSV( r===null ? this.rgb[0] : r, g===null ? this.rgb[1] : g, b===null ? this.rgb[2] : b ); if(hsv[0] !== null) { this.hsv[0] = Math.max(0.0, this.minH, Math.min(6.0, this.maxH, hsv[0])); } if(hsv[2] !== 0) { this.hsv[1] = hsv[1]===null ? null : Math.max(0.0, this.minS, Math.min(1.0, this.maxS, hsv[1])); } this.hsv[2] = hsv[2]===null ? null : Math.max(0.0, this.minV, Math.min(1.0, this.maxV, hsv[2])); // update RGB according to final HSV, as some values might be trimmed var rgb = HSV_RGB(this.hsv[0], this.hsv[1], this.hsv[2]); this.rgb[0] = rgb[0]; this.rgb[1] = rgb[1]; this.rgb[2] = rgb[2]; this.exportColor(flags); }; this.fromString = function(hex, flags) { var m = hex.match(/^\W*([0-9A-F]{3}([0-9A-F]{3})?)\W*$/i); if(!m) { return false; } else { if(m[1].length === 6) { // 6-char notation this.fromRGB( parseInt(m[1].substr(0,2),16) / 255, parseInt(m[1].substr(2,2),16) / 255, parseInt(m[1].substr(4,2),16) / 255, flags ); } else { // 3-char notation this.fromRGB( parseInt(m[1].charAt(0)+m[1].charAt(0),16) / 255, parseInt(m[1].charAt(1)+m[1].charAt(1),16) / 255, parseInt(m[1].charAt(2)+m[1].charAt(2),16) / 255, flags ); } return true; } }; this.toString = function() { return ( (0x100 | Math.round(255*this.rgb[0])).toString(16).substr(1) + (0x100 | Math.round(255*this.rgb[1])).toString(16).substr(1) + (0x100 | Math.round(255*this.rgb[2])).toString(16).substr(1) ); }; function RGB_HSV(r, g, b) { var n = Math.min(Math.min(r,g),b); var v = Math.max(Math.max(r,g),b); var m = v - n; if(m === 0) { return [ null, 0, v ]; } var h = r===n ? 3+(b-g)/m : (g===n ? 5+(r-b)/m : 1+(g-r)/m); return [ h===6?0:h, m/v, v ]; } function HSV_RGB(h, s, v) { if(h === null) { return [ v, v, v ]; } var i = Math.floor(h); var f = i%2 ? h-i : 1-(h-i); var m = v * (1 - s); var n = v * (1 - s*f); switch(i) { case 6: case 0: return [v,n,m]; case 1: return [n,v,m]; case 2: return [m,v,n]; case 3: return [m,n,v]; case 4: return [n,m,v]; case 5: return [v,m,n]; } } function removePicker() { delete jscolor.picker.owner; document.getElementsByTagName('body')[0].removeChild(jscolor.picker.boxB); } function drawPicker(x, y) { if(!jscolor.picker) { jscolor.picker = { box : document.createElement('div'), boxB : document.createElement('div'), pad : document.createElement('div'), padB : document.createElement('div'), padM : document.createElement('div'), sld : document.createElement('div'), sldB : document.createElement('div'), sldM : document.createElement('div'), btn : document.createElement('div'), btnS : document.createElement('span'), btnT : document.createTextNode(THIS.pickerCloseText) }; for(var i=0,segSize=4; i:Q0 ~Ɔ~r0hob z~Hy μ>zkU{C(aȅ^ [hvu c׈G{"?23:R z3 vF AZ~3n=R EZɱI"uXy~@0DMbw5Fw71=?ʦS,:tq03fb޹2jS @aD9&e,1C4$ONttB_lAEQ4Gilt1ڀHvhob>g&_Hen/kSzHK,_frǛ]3$\υIZ _ڀtقR~lB[?AWhh%\Yۓ'/+2΀v% _TQ3ݘ<ڛXYVןvV^g_( 8՟>:ޮ_ΪU)~]ԯ3B8=y#h↵X+9F~^' Ias!]h"č[9kY@0L1Q0?ڛM<*pTB*f$lz3W4[I]OZ'o%co7mhv0)a@eBj]UQ/|4߮CoZv]Ruv]);5,t[Ю'_;' Ў'__O/ .fm.%9b>MzyBꩼ D A/k-;oQubmm,yC A/qNboZI"(F}ef(j*CP^'f\?(eZ_W&{c6 ӡMivBh_6lPebp\VuwrHbU,̹>s]%0muB//ς O{-(Zgqā=:y{.Gia! { 'QBz5Iq's 7 KxV۠G> Q}ͯz?A{BGͽШ΅G*,>{J AKk w0O%PVtMKz@iy7d:4@KjN:SwUml R_T#t1Ewb ҳtGmi Ů]0hWb #G0< j0b T0SG]B5cwn!JV ~#c<isa/Vq>q;PR?g/`ͣXà0h! | QٯRz1_Tmum$s11JҾMv00b_*&sЦ;#Bc>>-M'F7i)dLW m%NqP?6{MGr30{ib=LAw~Lg@GA'w_>Mh Nv"vCuZw|Ho^cg/i9kU"9ڕؑI·hJU׮@'+QQwtjAϾ`x+qtIENDB`RLumShiny/inst/www/jscolor/hs.png0000644000176200001440000000517412743662035016557 0ustar liggesusersPNG  IHDRe5 CIDATxr#+ Ea?%yH.qzj ,=;<*숽"}GԩuwaxkձҏgC2qosEK4 8 ڙ֏˪uu"hb{ŸKlXcU\cwRǟ; z 14QV x=sυKlGY+c$݈=0<= z;4EK 7FFC@"]VݿO aiFG"(€!G48F t@$ Ca_"\_2v&v&^2TaO?z 1tJ7#fʠ|F?$.#6lS`U?zt[:1neh$NWYн.# Z1`=ڟZ8[J`zAA]|t}0Gj{vU=MIsI1Јn{ "-͟v >p[c #`+N SjʕY~(_B~P-н[k_RVܿ}.?=t]*7`13]k_/Ov&vfΡnIdzC#.TX|5V? }4B W%(0-D? #n q8km*&khgb W`d*,-9o 秏HlM2g6|7$fzy [ ,(:DfJ'ҏx4CFF K4uY_?j,y"tRYQ"ÜQ}=*z OhfH=aD.D81Ҵ?ĊBxZYhD#\qtwS4&? ٞ>ϻ/zGthb{hEePZW͎vC]{#c8aEj$-Ь} _Թ8ړ 2J؆4GDi4@ K7iivlk1UgDgl#5t~'Q҄y# tbmUU6>ڟݿR9f܀gtBl FVFI_lW?Hlcn B;BK6wgTPwBGg:U?El =G2b6x?=Tle4ȯ]Q%\z @hrjA< {E_{ `y]^~0hVA6RHxE0-ʠ˚}y.j.nQ 8ڟlEY@σBl q cZ9-a6bwlѽO_w#v4Ƕ=Ԥ/ЏX$Rܭ\{/(,H4ҏC@J¬n22U=6p?=} zV8 I3A[Rяà] s WoxuS @-Ѕ~L 묌L`]Z?N$#(dnyLd .1WZ%z0G֏@}R2:A+_DO.sÇ%҅~P,ٛ+|"us[:ڟbDMez(gٗ |F#W1л-kB 0wB2#9ڍT4跏c7A@Jr5Țĩ̹q Ol }_@x2)Sz|8ڟIk2+|MFp&' tGuj؆oxFb3Z?(s̗{t݂܉Nה[FdꚜLdbӡn.е~0_>ҼȖ d'Jv }?>Ė! -H: KIENDB`RLumShiny/inst/www/jscolor/cross.gif0000644000176200001440000000012312743662035017244 0ustar liggesusersGIF89a! ,$ǝRQg/,@))qڤp Panel will not be shown headerPanel(title = NULL), # 2- width = 5 -> refers to twitters bootstrap grid system # where the the maximum width is 12 that is to be shared between all # elements sidebarPanel(width = 5, # include a tabs in the input panel for easier navigation tabsetPanel(id = "tabs", type = "pill", selected = "Data", # Tab 1: Data input tabPanel("Data", # informational text div(align = "center", h5("Data upload")), # file upload button (data set 1) fileInput(inputId = "file1", label = strong("Primary data set"), accept="text/plain"), tooltip(refId = "file1", text = tags$img(src='file_structure.png', width='250px')), # file upload button (data set 2) fileInput(inputId = "file2", label = strong("Secondary data set"), accept="text/plain"), tooltip(refId = "file2", text = tags$img(src='file_structure.png', width='250px')), # informational text div(align = "center", h5("Settings")), fluidRow( column(width = 6, # logical: should NA values be excluded? checkboxInput(inputId = "naExclude", label = "Exclude NA values", value = TRUE), tooltip(refId = "naExclude", text = "Exclude NA values from the data set prior to any further operations.") ), column(width = 6, # logical: file contains headers? checkboxInput(inputId = "headers", label = "File contains headers", value = FALSE), tooltip(refId = "headers", text = tags$img(src='file_containsHeader.png', width='250px')) )), # char: columns separated by tab, space, comma radioButtons("sep", "Separator", selected = "\t", inline = TRUE, c("Tab" = "\t", "Space" = " ", "Comma" = ",", "Semicolon" = ";")), tooltip(refId = "sep", text = tags$img(src='file_sep.png', width='400px'), placement = "auto left"), hr(), actionButton(inputId = "refresh", label = "Refresh", icon = icon("refresh")), tooltip(refId = "refresh", text = "Redraw the plot") ),##EndOf::Tab_1 # Tab 2: Statistical information tabPanel("Statistics", div(align = "center", h5("Summary")), fluidRow( column(width = 6, checkboxInput(inputId = "summary", label = "Show summary", value = FALSE), tooltip(refId = "summary", text = "Adds numerical output to the plot") ), column(width = 6, selectInput(inputId = "sumpos", label = "Summary position", selected = "topleft", choices = list("Subtitle" = "sub", "Center" = "center", Top=c("Top" = "top", "Top left" = "topleft", "Top right"= "topright"), Bottom=c("Bottom" = "bottom", "Bottom left" = "bottomleft", "Bottom right" = "bottomright") )), tooltip(refId = "sumpos", attr = "for", text = "Position of the statistical summary. The keyword \"Subtitle\" will only work if no plot subtitle is used.") ) ), checkboxGroupInput(inputId = "stats", label = "Parameters", selected = c("n","mean"), choices = c("n" = "n", "Mean" = "mean", "weighted Mean" = "mean.weighted", "Median" = "median", "weighted Median" = "median.weighted", "rel. Standard deviation" = "sdrel", "abs. Standard deviation" = "sdabs", "rel. Standard error" = "serel", "abs. Standard error" = "seabs", #"25 % Quartile" = "q25", #not implemented yet #"75 % Quartile" = "q75", #not implemented yet "KDEmax" = "kdemax", "Skewness" = "skewness", "Kurtosis" = "kurtosis" )), tooltip(refId = "stats", text = "Statistical parameters to be shown in the summary"), br(), div(align = "center", h5("Datapoint labels")), div(align = "center", checkboxGroupInput(inputId = "statlabels", inline = TRUE, label = NULL, choices = c("Min" = "min", "Max" = "max", "Median" = "median"))), tooltip(refId = "statlabels", text = "Additional labels of statistically important values in the plot.") ),##EndOf::Tab_2 # Tab 3: input that refer to the plot rather than the data tabPanel("Plot", div(align = "center", h5("Title")), fluidRow( column(width = 6, textInput(inputId = "main", label = "Title", value = "Radial Plot") ), column(width = 6, textInput(inputId = "mtext", label = "Subtitle", value = "") ) ), div(align = "center", h5("Scaling")), fluidRow( column(width = 6, # inject sliderInput from Server.R uiOutput(outputId = "centValue"), tooltip(refId = "centValue", text = "User-defined central value, primarily used for horizontal centering of the z-axis") ), column(width = 6, sliderInput(inputId = "cex", label = "Scaling factor", min = 0.5, max = 2, value = 1.0, step = 0.1) ) ), selectInput(inputId = "centrality", label = "Centrality", list("Mean" = "mean", "Median" = "median", "Weighted mean" = "mean.weighted", "Weighted median" = "median.weighted")), tooltip(refId = "centrality", attr = "for", text = "Measure of centrality, used for the standardisation, centering the plot and drawing the central line.") ),##EndOf::Tab_3 # Tab 4: modify axis parameters tabPanel("Axis", div(align = "center", h5("X-axis")), fluidRow( column(width = 6, textInput(inputId = "xlab1", label = "Label x-axis (upper)", value = "Relative error [%]") ), column(width = 6, textInput(inputId = "xlab2", label = "Label x-axis (lower)", value = "Precision") ) ), # inject sliderInput from Server.R uiOutput(outputId = "xlim"), div(align = "center", h5("Y-axis")), checkboxInput(inputId = "yticks", label = HTML("Show ±2σ label"), value = TRUE), tooltip(refId = "yticks", text = "Option to hide y-axis labels."), textInput(inputId = "ylab", label = "Label y-axis", value = "Standardised estimate"), div(align = "center", h5("Z-axis")), checkboxInput(inputId = "logz", label = "Logarithmic z-axis", value = TRUE), tooltip(refId = "logz", text = "Option to display the z-axis in logarithmic scale."), textInput(inputId = "zlab", label = "Label z-axis", value = "Equivalent dose [Gy]"), # inject sliderInput from Server.R uiOutput(outputId = "zlim"), sliderInput('curvature', 'Z-axis curvature', min=0, max=3, value=4.5/5.5, step=0.01, round=FALSE), tooltip(refId = "curvature", attr = "for", text = "User-defined plot area ratio (i.e. curvature of the z-axis). If omitted, the default value (4.5/5.5) is used and modified automatically to optimise the z-axis curvature. The parameter should be decreased when data points are plotted outside the z-axis or when the z-axis gets too elliptic.") ),##EndOf::Tab_4 # Tab 5: modify data point representation tabPanel("Datapoints", div(align = "center", h5("Primary data set")), fluidRow( column(width = 6, selectInput(inputId = "pch", label = "Style", selected = "17", choices = c("Square"= "1", "Circle"="2", "Triangle point up"="3", "Plus"="4", "Cross"="5", "Diamond"="6", "Triangle point down"="7", "Square cross"="8", "Star"="9", "Diamond plus"="10", "Circle plus"="11", "Triangles up and down"="12", "Square plus"="13", "Circle cross"="14", "Square and Triangle down"="15", "filled Square"="16", "filled Circle"="17", "filled Triangle point up"="18", "filled Diamond"="19", "solid Circle"="20", "Bullet (smaller Circle)"="21", "Custom"="custom")) ), column(width = 6, # show only if custom symbol is desired conditionalPanel(condition = "input.pch == 'custom'", textInput(inputId = "custompch", label = "Insert character", value = "?")) ) ), fluidRow( column(width = 6, selectInput(inputId = "color", label = "Datapoint color", choices = list("Black" = "black", "Grey" = "grey50", "Red" = "#b22222", "Green" = "#6E8B3D", "Blue" = "#428bca", "Custom" = "custom")) ), column(width = 6, # show only if custom color is desired conditionalPanel(condition = "input.color == 'custom'", jscolorInput(inputId = "rgb", label = "Choose a color")) ) ), div(align = "center", h5("Secondary data set")), fluidRow( column(width = 6, ## DATA SET 2 selectInput(inputId = "pch2", label = "Style", selected = "17", choices = c("Square"= "1", "Circle"="2", "Triangle point up"="3", "Plus"="4", "Cross"="5", "Diamond"="6", "Triangle point down"="7", "Square cross"="8", "Star"="9", "Diamond plus"="10", "Circle plus"="11", "Triangles up and down"="12", "Square plus"="13", "Circle cross"="14", "Square and Triangle down"="15", "filled Square"="16", "filled Circle"="17", "filled Triangle point up"="18", "filled Diamond"="19", "solid Circle"="20", "Bullet (smaller Circle)"="21", "Custom"="custom")) ), column(width = 6, # show only if custom symbol is desired conditionalPanel(condition = "input.pch2 == 'custom'", textInput(inputId = "custompch2", label = "Insert character", value = "?")) ) ), fluidRow( column(width = 6, selectInput(inputId = "color2", label = "Datapoint color", selected = "#b22222", choices = list("Black" = "black", "Grey" = "grey50", "Red" = "#b22222", "Green" = "#6E8B3D", "Blue" = "#428bca", "Custom" = "custom")) ), column(width = 6, # show only if custom color is desired conditionalPanel(condition = "input.color2 == 'custom'", jscolorInput(inputId = "rgb2", label = "Choose a color")) ) ) ),##EndOf::Tab_5 # Tab 6: add additional lines to the plot tabPanel("Lines", helpText("Here you can add additional lines."), # options for custom lines: # 1 - z-value, 2 - color, 3 - label # only the options for the first line are shown numericInput(inputId = "line1", label = strong("Line #1"), value = NA, min = 0), tooltip(refId = "line1", text = "Numeric values of the additional lines to be added."), fluidRow( column(width = 6, HTML("Choose a color
"), jscolorInput(inputId = "colline1") ), column(width = 6, textInput(inputId = "labline1", label = "Label", value = "") ) ), # conditional chain: if valid input (i.e. the z-value is > 0) is provided # for the previous line, show options for a new line (currently up to eight) conditionalPanel(condition = "input.line1 > 0", numericInput(inputId = "line2", strong("Line #2"), NA, min = 0), fluidRow( column(width = 6, HTML("Choose a color
"),jscolorInput(inputId = "colline2")), column(width = 6, textInput("labline2","Label",value = "")) ) ), conditionalPanel(condition = "input.line2 > 0", numericInput(inputId = "line3", strong("Line #3"), NA, min = 0), fluidRow( column(width = 6, HTML("Choose a color
"),jscolorInput(inputId = "colline3")), column(width = 6, textInput("labline3","Label",value = "")) ) ), conditionalPanel(condition = "input.line3 > 0", numericInput(inputId = "line4", strong("Line #4"), NA, min = 0), fluidRow( column(width = 6, HTML("Choose a color
"),jscolorInput(inputId = "colline4")), column(width = 6, textInput("labline4","Label",value = "")) ) ), conditionalPanel(condition = "input.line4 > 0", numericInput(inputId = "line5", strong("Line #5"), NA, min = 0), fluidRow( column(width = 6, HTML("Choose a color
"),jscolorInput(inputId = "colline5")), column(width = 6, textInput("labline5","Label",value = "")) ) ), conditionalPanel(condition = "input.line5 > 0", numericInput(inputId = "line6", strong("Line #6"), NA, min = 0), fluidRow( column(width = 6, HTML("Choose a color
"),jscolorInput(inputId = "colline6")), column(width = 6, textInput("labline6","Label",value = "")) ) ), conditionalPanel(condition = "input.line6 > 0", numericInput(inputId = "line7", strong("Line #7"), NA, min = 0), fluidRow( column(width = 6, HTML("Choose a color
"),jscolorInput(inputId = "colline7")), column(width = 6, textInput("labline7","Label",value = "")) ) ), conditionalPanel(condition = "input.line7 > 0", numericInput(inputId = "line8", strong("Line #8"), NA, min = 0), fluidRow( column(width = 6, HTML("Choose a color
"),jscolorInput(inputId = "colline8")), column(width = 6, textInput("labline8","Label",value = "")) ) ) ),##EndOf::Tab_6 # Tab 7: modify the 2-sigma bar (radial plot), grid (both) and polygon (KDE) tabPanel("Bars & Grid", div(align = "center", h5("Central line")), fluidRow( column(width = 6, numericInput(inputId = "lwd", label = "Central line width #1", min = 0, max = 5, value = 1) ), column(width = 6, numericInput(inputId = "lwd2", label = "Central line width #2", min = 0, max = 5, value = 1) ) ), fluidRow( column(width = 6, selectInput(inputId = "lty", label = "Line type", selected = 2, choices = list("Blank" = 0, "Solid" = 1, "Dashed" = 2, "Dotted" = 3, "Dot dash" = 4, "Long dash" = 5, "Two dash" = 6)) ), column(width = 6, selectInput(inputId = "lty2", label = "Line type", selected = 2, choices = list("Blank" = 0, "Solid" = 1, "Dashed" = 2, "Dotted" = 3, "Dot dash" = 4, "Long dash" = 5, "Two dash" = 6)) ) ), div(align = "center", HTML("
2σ bar
")), fluidRow( column(width = 6, selectInput(inputId = "bar", label = HTML("2σ bar color"), choices = list("Grey" = "grey50", "Custom" = "custom", "None" = "none")) ), column(width = 6, selectInput(inputId = "bar2", label = HTML("2σ bar color #2"), choices = list("Grey" = "grey50", "Custom" = "custom", "None" = "none")) ) ), fluidRow( column(width = 6, # show only if custom color is desired conditionalPanel(condition = "input.bar == 'custom'", jscolorInput(inputId = "rgbBar", label = "Choose a color")) ), column(width = 6, # show only if custom color is desired conditionalPanel(condition = "input.bar2 == 'custom'", jscolorInput(inputId = "rgbBar2", label = "Choose a color")) ) ), sliderInput(inputId = "alpha.bar", label = "Transparency", min = 0, max = 100, step = 1, value = 66), div(align = "center", h5("Grid")), fluidRow( column(width = 6, selectInput("grid", "Grid color", list("Grey" = "grey", "Custom" = "custom", "None" = "none")), tooltip(refId = "grid", attr = "for", text = "colour of the grid lines (originating at [0,0] and stretching to the z-scale). To disable grid lines, use \"none\".") ), column(width = 6, # show only if custom color is desired conditionalPanel(condition = "input.grid == 'custom'", jscolorInput(inputId = "rgbGrid", label = "Choose a color")) ) ), sliderInput(inputId = "alpha.grid", label = "Transparency", min = 0, max = 100, step = 1, value = 100) ),##EndOf::Tab_7 tabPanel("Legend", div(align = "center", h5("Legend")), fluidRow( column(width = 6, checkboxInput(inputId = "showlegend", label = "Show legend", value = FALSE), tooltip(refId = "showlegend", text = "Legend content to be added to the plot.") ), column(width = 6, selectInput(inputId = "legend.pos", label = "Legend position", selected = "bottomleft", choices = c("Top" = "top", "Top left" = "topleft", "Top right"= "topright", "Center" = "center", "Bottom" = "bottom", "Bottom left" = "bottomleft", "Bottom right" = "bottomright")) ) ), fluidRow( column(width = 6, textInput(inputId = "legendname", label = "Primary data label", value = "primary data") ), column(width = 6, textInput(inputId = "legendname2", label = "Secondary data label", value = "secondary data") ) ) ),##EndOf::Tab_8 # Tab 9: save plot as pdf, wmf or eps tabPanel("Export", radioButtons(inputId = "fileformat", label = "Fileformat", selected = "pdf", choices = c("PDF (Portable Document Format)" = "pdf", "SVG (Scalable Vector Graphics)" = "svg", "EPS (Encapsulated Postscript)" = "eps")), textInput(inputId = "filename", label = "Filename", value = "Radial Plot"), fluidRow( column(width = 6, numericInput(inputId = "imgheight", label = "Image height", value = 7) ), column(width = 6, numericInput(inputId = "imgwidth", label = "Image width", value = 7) ) ), selectInput(inputId = "fontfamily", label = "Font", selected = "Helvetica", choices = c("Helvetica" = "Helvetica", "Helvetica Narrow" = "Helvetica Narrow", "Times" = "Times", "Courier" = "Courier", "Bookman" = "Bookman", "Palatino" = "Palatino")), tags$hr(), downloadButton(outputId = "exportFile", label = "Download plot"), tags$hr(), helpText("Additionally, you can download a corresponding .R file that contains", "a fully functional script to reproduce the plot in your R environment!"), downloadButton(outputId = "exportScript", label = "Download R script") ),##EndOf::Tab_8 # Tab 10: further information tabPanel("About", hr(), div(align = "center", # HTML code to include a .png file in the tab; the image file must be in # a subfolder called "wwww" img(src="RL_Logo.png", height = 100, width = 100, alt = "R.Lum"), p("Links:"), a(href = "http://www.r-luminescence.de", "R.Luminescence project page", target="_blank"), br(), a(href = "https://forum.r-luminescence.de", "Message board", target="_blank"), br(), a(href = "http://zerk.canopus.uberspace.de/R.Lum", "Online application", target="_blank"), br(),hr(), img(src='GitHub-Mark-32px.png', width='32px', height='32px'), br(), a(href = "https://github.com/tzerk/RLumShiny/tree/master/inst/shiny/radialplot", "See the code at GitHub!", target="_blank") )#/div )##EndOf::Tab_9 )##EndOf::tabsetPanel ),##EndOf::sidebarPanel # 3 - output panel mainPanel(width = 7, # insert css code inside of the generated HTML file: # allow open dropdown menus to reach over the container tags$head(tags$style(type="text/css",".tab-content {overflow: visible;}")), tags$head(includeCSS("www/style.css")), # divide output in separate tabs via tabsetPanel tabsetPanel( tabPanel("Plot", plotOutput(outputId = "main_plot", height = "500px")), tabPanel("Primary data set", dataTableOutput("dataset")), tabPanel("Secondary data set", dataTableOutput("dataset2")), tabPanel("Central Age Model", dataTableOutput("CAM")), tabPanel("R plot code", verbatimTextOutput("plotCode")) )###EndOf::tabsetPanel )##EndOf::mainPanel )##EndOf::shinyUI(pageWithSidebar)RLumShiny/inst/shiny/radialplot/server.R0000644000176200001440000004243612743662035020060 0ustar liggesusers## Server.R library(Luminescence) library(shiny) # load example data data(ExampleData.DeValues) data <- ExampleData.DeValues$CA1 ## MAIN FUNCTION shinyServer(function(input, output, session) { # check and read in file (DATA SET 1) datGet<- reactive({ inFile<- input$file1 if(is.null(inFile)) return(NULL) # if no file was uploaded return NULL return(read.table(file = inFile$datapath, # inFile[1] contains filepath sep = input$sep, quote = "", header = input$headers)) # else return file }) # check and read in file (DATA SET 2) datGet2<- reactive({ inFile2<- input$file2 if(is.null(inFile2)) return(NULL) # if no file was uploaded return NULL return(read.table(file = inFile2$datapath, # inFile[1] contains filepath sep = input$sep, quote = "", header = input$headers)) # else return file }) # dynamically inject sliderInput for central value output$centValue<- renderUI({ # check if file is loaded # # case 1: yes -> slinderInput with custom values if(!is.null(datGet())) { if(!is.null(datGet2())) { centValue.data<- rbind(datGet(),datGet2()) sliderInput(inputId = "centValue", label = "Central Value", min = min(centValue.data[,1])*0.9, max = max(centValue.data[,1])*1.1, value = mean(centValue.data[,1])) } else { data<- datGet() sliderInput(inputId = "centValue", label = "Central Value", min = min(data[,1])*0.9, max = max(data[,1])*1.1, value = mean(data[,1])) } } else { #case 2: no -> sliderInput for example data sliderInput(inputId = "centValue", label = "Central Value", min = min(data[,1])*0.9, max = max(data[,1])*1.1, value = mean(data[,1]), step = 1, round = 0) } })## EndOf::renderUI() # dynamically inject sliderInput for z-axis range output$xlim<- renderUI({ # check if file is loaded # # case 1: yes -> slinderInput with custom values if(!is.null(datGet())) { if(!is.null(datGet2())) { xlim.data<- rbind(datGet(),datGet2()) if(input$logz == TRUE) { sd<- xlim.data[,2] / xlim.data[,1] } else { sd<- xlim.data[,2] } prec<- 1/sd sliderInput(inputId = "xlim", label = "Range x-axis", min = 0, max = max(prec)*2, value = c(0, max(prec)*1.05), round=FALSE, step=0.0001) } else { data<- datGet() if(input$logz == TRUE) { sd<- data[,2] / data[,1] } else { sd<- data[,2] } prec<- 1/sd sliderInput(inputId = "xlim", label = "Range x-axis", min = 0, max = max(prec)*2, value = c(0, max(prec)*1.05), round=FALSE, step=0.0001) } } else { #case 2: no -> sliderInput for example data if(input$logz == TRUE) { sd<- data[,2] / data[,1] } else { sd<- data[,2] } prec<- 1/sd sliderInput(inputId = "xlim", label = "Range x-axis", min = 0, max = max(prec)*2, value = c(0, max(prec)*1.05), round=FALSE, step=0.0001) } })## EndOf::renderUI() # dynamically inject sliderInput for z-axis range output$zlim<- renderUI({ # check if file is loaded # # case 1: yes -> slinderInput with custom values if(!is.null(datGet())) { if(!is.null(datGet2())) { zlim.data<- rbind(datGet(),datGet2()) sliderInput(inputId = "zlim", label = "Range z-axis", min = min(zlim.data[,1])*0.25, max = max(zlim.data[,1])*1.75, value = c(min(zlim.data[,1])*0.8, max(zlim.data[,1])*1.2)) } else { data<- datGet() sliderInput(inputId = "zlim", label = "Range z-axis", min = min(data[,1])*0.25, max = max(data[,1])*1.75, value = c(min(data[,1])*0.8, max(data[,1])*1.2)) } } else { #case 2: no -> sliderInput for example data sliderInput(inputId = "zlim", label = "Range z-axis", min = min(data[,1])*0.25, max = max(data[,1])*1.75, value = c(min(data[,1])*0.8, max(data[,1]))*1.2, step = 1, round = 0) } })## EndOf::renderUI() # render Radial Plot output$main_plot <- renderPlot({ # refresh plot on button press input$refresh # progress bar progress<- Progress$new(session, min = 0, max = 5) progress$set(message = "Calculation in progress", detail = "Retrieve data") on.exit(progress$close()) # make sure that input panels are registered on non-active tabs. # by default tabs are suspended and input variables are hence # not available outputOptions(x = output, name = "zlim", suspendWhenHidden = FALSE) outputOptions(x = output, name = "centValue", suspendWhenHidden = FALSE) outputOptions(x = output, name = "xlim", suspendWhenHidden = FALSE) # check if file is loaded and overwrite example data if(!is.null(datGet())) { data<- datGet() } if(!is.null(datGet2())) { data2<- datGet2() } if(is.null(datGet()) == FALSE && is.null(datGet2()) == FALSE) { data<- datGet() data2<- datGet2() data<- list(data, data2) } progress$set(value = 1) progress$set(message = "Calculation in progress", detail = "Get values") # check if any summary stats are activated, else NA if (input$summary) { summary<- input$stats } else { summary<- NA } # if custom datapoint color get RGB code from separate input panel if(input$color == "custom") { color<- input$rgb } else { color<- input$color } if(!is.null(datGet2())) { # if custom datapoint color get RGB code from separate input panel if(input$color2 == "custom") { color2<- input$rgb2 } else { color2<- input$color2 } } else { color2<- adjustcolor("white", alpha.f = 0) } # if custom datapoint style get char from separate input panel if(input$pch == "custom") { pch<- input$custompch } else { pch<- as.integer(input$pch)-1 #-1 offset in pch values } # if custom datapoint style get char from separate input panel if(input$pch2 == "custom") { pch2<- input$custompch2 } else { pch2<- as.integer(input$pch2)-1 #-1 offset in pch values } # workaround to initialize plotting after app startup if(is.null(input$centValue)) { centValue<- 3000 } else { centValue<- input$centValue } # update progress bar progress$set(value = 2) progress$set(message = "Calculation in progress", detail = "Combine values") # create numeric vector of lines line<- as.numeric(c(input$line1, input$line2, input$line3, input$line4, input$line5, input$line6, input$line7, input$line8)) # create char vector of line colors line.col<- c(input$colline1, input$colline2, input$colline3, input$colline4, input$colline5, input$colline6, input$colline7, input$colline8) # create char vector of line labels line.label<- c(input$labline1, input$labline2, input$labline3, input$labline4, input$labline5, input$labline6, input$labline7, input$labline8) # update progress bar progress$set(value = 3) progress$set(message = "Calculation in progress", detail = "Get values") # if custom bar color get RGB from separate input panel or "none" if(input$bar == "custom") { bar.col<- adjustcolor(col = input$rgbBar, alpha.f = input$alpha.bar/100) } else { if(input$bar == "none") { bar.col<- input$bar } else { bar.col<- adjustcolor(col = input$bar, alpha.f = input$alpha.bar/100) } } # if custom bar color get RGB from separate input panel or "none" # SECONDARY DATA SET if(input$bar2 == "custom") { bar.col2<- adjustcolor(col = input$rgbBar2, alpha.f = input$alpha.bar/100) } else { if(input$bar2 == "none") { bar.col2<- input$bar } else { bar.col2<- adjustcolor(col = input$bar2, alpha.f = input$alpha.bar/100) } } # if custom grid color get RGB from separate input panel or "none" if(input$grid == "custom") { grid.col<- adjustcolor(col = input$rgbGrid, alpha.f = input$alpha.grid/100) } else { if(input$grid == "none") { grid.col<- input$grid } else { grid.col<- adjustcolor(col = input$grid, alpha.f = input$alpha.grid/100) } } # update progress bar progress$set(value = 4) progress$set(message = "Calculation in progress", detail = "Almost there...") # workaround: if no legend wanted set label to NA and hide # symbol on coordinates -999, -999 if(input$showlegend == FALSE) { legend<- c(NA,NA) legend.pos<- c(-999,-999) } else { if(!is.null(datGet2())) { legend<- c(input$legendname, input$legendname2) legend.pos<- input$legend.pos } else { legend<- c(input$legendname, "") legend.pos<- input$legend.pos } } # validate(need()) makes sure that all data are available to # renderUI({}) before plotting and will wait until there validate( need(expr = input$centValue, message = 'Waiting for data... Please wait!'), need(expr = input$zlim, message = 'Waiting for data... Please wait!') ) progress$set(value = 5) progress$set(message = "Calculation in progress", detail = "Ready to plot") # plot radial Plot args <- list(data = data, xlim = input$xlim, zlim = input$zlim, xlab = c(input$xlab1, input$xlab2), ylab = input$ylab, zlab = input$zlab, y.ticks = input$yticks, grid.col = grid.col, bar.col = c(bar.col, bar.col2), pch = c(pch,pch2), col = c(color,color2), line = line, line.col = line.col, line.label = line.label, main = input$main, cex = input$cex, mtext = input$mtext, log.z = input$logz, stats = input$statlabels, plot.ratio = input$curvature, summary = summary, summary.pos = input$sumpos, legend = legend, legend.pos = legend.pos, na.rm = input$naExclude, central.value = input$centValue, centrality = input$centrality, lwd = c(input$lwd, input$lwd2), lty = c(as.integer(input$lty), as.integer(input$lty2))) do.call(plot_RadialPlot, args = args) # prepare code as text output if (is.null(input$sep)) updateRadioButtons(session, "fileformat", selected = "\t") if(input$sep == "\t") verb.sep<- "\\t" else verb.sep<- input$sep str1 <- paste("data <- read.delim(file, header = ",input$headers, ", sep= '", verb.sep,"')", sep = "") if(!is.null(datGet2())) { str2 <- "file2<- file.choose()" str3 <- paste("data2 <- read.delim(file2, header = ",input$headers, ", sep= '", verb.sep,"')", sep= "") str4 <- "data<- list(data, data2)" str1 <- paste(str1, str2, str3, str4, sep = "\n") } header <- paste("# To reproduce the plot in your local R environment", "# copy and run the following code to your R console.", "library(Luminescence)", "file<- file.choose()", str1, "\n", sep = "\n") names <- names(args) verb.arg <- paste(mapply(function(name, arg) { if (all(inherits(arg, "character"))) arg <- paste0("'", arg, "'") if (length(arg) > 1) arg <- paste0("c(", paste(arg, collapse = ", "), ")") if (is.null(arg)) arg <- "NULL" paste(name, "=", arg) }, names[-1], args[-1]), collapse = ",\n") funCall <- paste0("plot_RadialPlot(data = data,\n", verb.arg, ")") code.output <- paste0(header, funCall, collapse = "\n") # nested renderText({}) for code output on "R plot code" tab output$plotCode<- renderText({ code.output })##EndOf::renderText({}) output$exportScript <- downloadHandler( filename = function() { paste(input$filename, ".", "R", sep="") }, content = function(file) { write(code.output, file) },#EO content =, contentType = "text" )#EndOf::dowmloadHandler() # nested downloadHandler() to print plot to file output$exportFile <- downloadHandler( filename = function() { paste(input$filename, ".", input$fileformat, sep="") }, content = function(file) { # determine desired fileformat and set arguments if(input$fileformat == "pdf") { pdf(file, width = input$imgwidth, height = input$imgheight, paper = "special", useDingbats = FALSE, family = input$fontfamily) } if(input$fileformat == "svg") { svg(file, width = input$imgwidth, height = input$imgheight, family = input$fontfamily) } if(input$fileformat == "eps") { postscript(file, width = input$imgwidth, height = input$imgheight, paper = "special", family = input$fontfamily) } # plot radial Plot do.call(plot_RadialPlot, args = args) dev.off() },#EO content =, contentType = "image" )#EndOf::dowmloadHandler() })##EndOf::renderPlot({}) # renderTable() that prints the data to the second tab output$dataset<- renderDataTable( options = list(pageLength = 10, autoWidth = FALSE), callback = "function(table) { table.on('click.dt', 'tr', function() { $(this).toggleClass('selected'); Shiny.onInputChange('rows', table.rows('.selected').data().toArray()); }); }", { if(!is.null(datGet())) { data<- datGet() colnames(data)<- c("De","De error") data } else { colnames(data)<- c("De","De error") data } })##EndOf::renterTable() # renderTable() that prints the secondary data to the second tab output$dataset2<- renderDataTable( options = list(pageLength = 10, autoWidth = FALSE), callback = "function(table) { table.on('click.dt', 'tr', function() { $(this).toggleClass('selected'); Shiny.onInputChange('rows', table.rows('.selected').data().toArray()); }); }", { if(!is.null(datGet2())) { data<- datGet2() colnames(data)<- c("De","De error") data } else { } })##EndOf::renterTable() # renderTable() to print the results of the # central age model (CAM) output$CAM<- renderDataTable( options = list(pageLength = 10, autoWidth = FALSE), { if(!is.null(datGet())) { if(!is.null(datGet2())) { data<- list(datGet(), datGet2()) } else { data<- list(datGet()) } } else { data<- list(data) } t<- as.data.frame(matrix(nrow = length(data), ncol = 7)) colnames(t)<- c("Data set","n", "log data", "Central dose", "SE abs.", "OD (%)", "OD error (%)") res<- lapply(data, function(x) { calc_CentralDose(x, verbose = FALSE, plot = FALSE) }) for(i in 1:length(res)) { t[i,1]<- ifelse(i==1,"pimary","secondary") t[i,2]<- length(res[[i]]@data$data[,1]) t[i,3]<- res[[i]]@data$args$log t[i,4:7]<- round(res[[i]]@data$summary[1:4],2) } t })##EndOf::renterTable() })##EndOf::shinyServer(function(input, output)RLumShiny/inst/shiny/radialplot/www/0000755000176200001440000000000012743662035017242 5ustar liggesusersRLumShiny/inst/shiny/radialplot/www/GitHub-Mark-32px.png0000644000176200001440000000326212743662035022617 0ustar liggesusersPNG  IHDR szztEXtSoftwareAdobe ImageReadyqe<$iTXtXML:com.adobe.xmp $IDATxėmhayL30A+R#f>IHکy(M)_o5 0+0Ėl&o{i^]u<{Yws}=uC>$L, }<w}8^ AO?p! xaяPKI3`'B>0QT1<+`}^nvkp^ƅF|1"Gp.*oO׀Vp ]߅jc8K$q 8jV`#`vmpGѢu!#}#:U_?_yhE $=;c*xNOo+&w)%K-R%6n'o">j/t³qoGW7j%2q GX?woibCÐAzbǰt \14|S.DZ]# b|H$(ʕohmqͱRP셣$,0Z20 tNvRW3K8Xk2 IO6F)X6of-/OK S, r RY~ApO|xˉN;@NZYJgnܟ) ߍz?\:qD/ Rz攟:})%8Cgo;ކ"Ғ͏JiYL!3czOϘiENr!/K(R "r옷lþ9nȉ'TxCP1N"9A]ՇW AANƗ}Ú.GJͥ:fx/kS//gtSusw)mo{[g|APS+z;~ѱߗ(ZU|%?{=vi! 5.^3 $v` uTAz(bs59$\{e3_dW_d S(9w{o[۶==v99!-@ x4X_?1_בr3B)@{r:M+ͤQTJEnXPckAEPS2NRJ5Q/ԶmYo/gT)(._qwi ǽѻadЋ\r !P-}1(*$yy !)R "a%_ +GPSh1!T/5ewR0[_=1_=N㼉!tpЛWZ+"S #w{_ ߼/nI6F9KڛhoחA0RD 5;Wo;qD;S?U)&$S-ȕ~eꎿ?9{N8#RzUYJ痟:obdr'*$_'<|9Gt $Wx^_PԆ5%e1=VNURLͯGK{ ^_<32!r YR }!}!"5Żmc?>㞿}R:WO9( i&}+I))=ϛuD/T _|5SQ@K!)EL 5l5sm ANRmAU/T j D!l \SR1[ .@P}L5АkAKǗUnX u?߻=_љ)+dBZYU2uԖ@~Q/eW_|=?~dݞ'Nhgd@}R*!,?u؛h Dɬ־usK;fx >zE=w2?)5HiFc`UP/T!AYxAEN]U)ݤ('TEP 洟?]?GN&[RB)fC?=FP 'D8KOӸm(R MA}OPBs#BAP;z!\h!,{*˱ci}?r qB(iRWv z dQ^ȜJ}BS@PB~^gu[;STJ+eR\GJ_qP#ˑSȳ{kHG>׎/+QqyN{%^[OzUP[*r bWӠ}R 7 o{w۶ǂ^DT5tWnS~갿 EHI)S=ϛuD%߲-j^)@KiHlkHBU%[W#-#)@k٧M)=okRZOP^-9ȷ]MDJGT)HT?" iB7;ez" "G֤U(-/_wǼ{eA}S OI D%ޒ[bj[BcVR3QSB]v%Ҷ<"YYIc7.텪TGPT } W#t˃E,[ʇ{JeAU/EƟ#}])EL&P/T ꭃLw*jUPS2)&F/56+#ٴo[l˹EP/T m~x% ^)@"?ncS\/2D%/GV_P#P;Y˛8ɥ/M\0}oKLmKZLz.ے7n[@ HJیS˛RX?c^he|\Ҏ^^oVS2h:#RZY0^(EAPWvTAˬ*r "d$AU5 u  ;H鱲nhNH+Ŗ\@@LYP HHґRh+*J,%A}Oz-PJkDNNǛHMYp,. 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The keyword \"Subtitle\" will only work if no plot subtitle is used."), checkboxGroupInput(inputId = "stats", label = "Parameters", selected = c("n","mean"), choices = c("n" = "n", "Mean" = "mean", "weighted Mean" = "mean.weighted", "Median" = "median", #"weighted Median" = "median.weighted", "rel. Standard deviation" = "sdrel", "abs. Standard deviation" = "sdabs", "rel. Standard error" = "serel", "abs. Standard error" = "seabs", #"25 % Quartile" = "q25", #not implemented yet #"75 % Quartile" = "q75", #not implemented yet "Skewness" = "skewness", #not implemented yet "Kurtosis" = "kurtosis", #not implemented yet "Confidence interval" = "in.ci")), tooltip(refId = "stats", text = "Statistical parameters to be shown in the summary"), br(), div(align = "center", h5("Error range")), numericInput(inputId = "error", label = "Symmetric error range (%)", value = 10, min = 0, max = 100, step = 1), tooltip(refId = "error", text = "Symmetric error range in percent will be shown as dashed lines in the plot. Set error.range to 0 to void plotting of error ranges.") ),##EndOf::Tab_2 # Tab 3: input that refer to the plot rather than the data tabPanel("DRT Details", div(align = "center", h5("Experimental details")), numericInput(inputId = "dose", label = "Given dose (primary data set)", value = 2800), tooltip(refId = "dose", text = "Given dose used for the dose recovery test to normalise data. If only one given dose is provided this given dose is valid for all input data sets (i.e., values is a list). Otherwise a given dose for each input data set has to be provided (e.g., given.dose = c(100,200)). If no given.dose values are plotted without normalisation (might be useful for preheat plateau tests). Note: Unit has to be the same as from the input values (e.g., Seconds or Gray)."), numericInput(inputId = "dose2", label = "Given dose (secondary data set)", value = 3000), div(align = "center", h5("Preheat temperatures")), checkboxInput(inputId = "preheat", label = "Group values by preheat temperature", FALSE), tooltip(refId = "preheat", text = "Optional preheat temperatures to be used for grouping the De values. If specified, the temperatures are assigned to the x-axis."), conditionalPanel(condition = 'input.preheat == true', numericInput(inputId = "ph1", "PH Temperature #1", 180, min = 0), numericInput(inputId = "ph2", "PH Temperature #2", 200, min = 0), numericInput(inputId = "ph3", "PH Temperature #3", 220, min = 0), numericInput(inputId = "ph4", "PH Temperature #4", 240, min = 0), numericInput(inputId = "ph5", "PH Temperature #5", 260, min = 0), numericInput(inputId = "ph6", "PH Temperature #6", 280, min = 0), numericInput(inputId = "ph7", "PH Temperature #7", 300, min = 0), numericInput(inputId = "ph8", "PH Temperature #8", 320, min = 0) ) ),##EndOf::Tab_3 # Tab 3: input that refer to the plot rather than the data tabPanel("Plot", div(align = "center", h5("Title")), fluidRow( column(width = 6, textInput(inputId = "main", label = "Title", value = "DRT Plot") ), column(width = 6, textInput(inputId = "mtext", label = "Subtitle", value = "") ) ), div(align = "center", h5("Boxplot")), checkboxInput(inputId = "boxplot", label = "Plot as boxplot", value = FALSE), tooltip(refId = "boxplot", text = "Optionally plot values, that are grouped by preheat temperature as boxplots. Only possible when preheat vector is specified."), div(align = "center", h5("Scaling")), sliderInput(inputId = "cex", label = "Scaling factor", min = 0.5, max = 2, value = 1.0, step = 0.1) ),##EndOf::Tab_3 # Tab 4: modify axis parameters tabPanel("Axis", div(align = "center", h5("X-axis")), textInput(inputId = "xlab", label = "Label x-axis", value = "# Aliquot"), # inject sliderInput from Server.R uiOutput(outputId = "xlim"), br(), div(align = "center", h5("Y-axis")), textInput(inputId = "ylab", label = "Label y-axis", value = "Normalised De"), sliderInput(inputId = "ylim", label = "Range y-axis", min = 0, max = 3, value = c(0.75, 1.25), step = 0.01) ),##EndOf::Tab_4 tabPanel("Datapoints", div(align = "center", h5("Primary data set")), fluidRow( column(width = 6, selectInput(inputId = "pch", label = "Style", selected = "17", choices = c("Square"= "1", "Circle"="2", "Triangle point up"="3", "Plus"="4", "Cross"="5", "Diamond"="6", "Triangle point down"="7", "Square cross"="8", "Star"="9", "Diamond plus"="10", "Circle plus"="11", "Triangles up and down"="12", "Square plus"="13", "Circle cross"="14", "Square and Triangle down"="15", "filled Square"="16", "filled Circle"="17", "filled Triangle point up"="18", "filled Diamond"="19", "solid Circle"="20", "Bullet (smaller Circle)"="21", "Custom"="custom")) ), column(width = 6, # show only if custom symbol is desired conditionalPanel(condition = "input.pch == 'custom'", textInput(inputId = "custompch", label = "Insert character", value = "?")) ) ), fluidRow( column(width = 6, selectInput(inputId = "color", label = "Datapoint color", choices = list("Black" = "black", "Grey" = "grey50", "Red" = "#b22222", "Green" = "#6E8B3D", "Blue" = "#428bca", "Custom" = "custom")) ), column(width = 6, # show only if custom color is desired conditionalPanel(condition = "input.color == 'custom'", jscolorInput(inputId = "rgb", label = "Choose a color")) ) ), br(), div(align = "center", h5("Secondary data set")), fluidRow( column(width = 6, ## DATA SET 2 selectInput(inputId = "pch2", label = "Style", selected = "17", choices = c("Square"= "1", "Circle"="2", "Triangle point up"="3", "Plus"="4", "Cross"="5", "Diamond"="6", "Triangle point down"="7", "Square cross"="8", "Star"="9", "Diamond plus"="10", "Circle plus"="11", "Triangles up and down"="12", "Square plus"="13", "Circle cross"="14", "Square and Triangle down"="15", "filled Square"="16", "filled Circle"="17", "filled Triangle point up"="18", "filled Diamond"="19", "solid Circle"="20", "Bullet (smaller Circle)"="21", "Custom"="custom")) ), column(width = 6, # show only if custom symbol is desired conditionalPanel(condition = "input.pch2 == 'custom'", textInput(inputId = "custompch2", label = "Insert character", value = "?")) ) ), fluidRow( column(width = 6, selectInput(inputId = "color2", label = "Datapoint color", selected = "#b22222", choices = list("Black" = "black", "Grey" = "grey50", "Red" = "#b22222", "Green" = "#6E8B3D", "Blue" = "#428bca", "Custom" = "custom")) ), column(width = 6, # show only if custom color is desired conditionalPanel(condition = "input.color2 == 'custom'", jscolorInput(inputId = "rgb2", label = "Choose a color")) ) ) ),##EndOf::Tab_5 # Tab xy: add and customize legend tabPanel("Legend", div(align = "center", h5("Legend")), fluidRow( column(width = 6, textInput(inputId = "legendname", label = "Primary data label", value = "primary data") ), column(width = 6, textInput(inputId = "legendname2", label = "Secondary data label", value = "secondary data") ) ), selectInput(inputId = "legend.pos", label = "Legend position", selected = "bottomleft", choices = c("Top" = "top", "Top left" = "topleft", "Top right"= "topright", "Center" = "center", "Bottom" = "bottom", "Bottom left" = "bottomleft", "Bottom right" = "bottomright")) ),##EndOf::Tab_xy # Tab xy: save plot as pdf, wmf or eps tabPanel("Export", radioButtons(inputId = "fileformat", label = "Fileformat", selected = "pdf", choices = c("PDF (Portable Document Format)" = "pdf", "SVG (Scalable Vector Graphics)" = "svg", "EPS (Encapsulated Postscript)" = "eps")), textInput(inputId = "filename", label = "Filename", value = "DRT Plot"), fluidRow( column(width = 6, numericInput(inputId = "imgheight", label = "Image height", value = 7) ), column(width = 6, numericInput(inputId = "imgwidth", label = "Image width", value = 7) ) ), selectInput(inputId = "fontfamily", label = "Font", selected = "Helvetica", choices = c("Helvetica" = "Helvetica", "Helvetica Narrow" = "Helvetica Narrow", "Times" = "Times", "Courier" = "Courier", "Bookman" = "Bookman", "Palatino" = "Palatino")), tags$hr(), downloadButton(outputId = "exportFile", label = "Download plot") ),##EndOf::Tab_ # Tab xy: further information tabPanel("About", hr(), div(align = "center", # HTML code to include a .png file in the tab; the image file must be in # a subfolder called "wwww" img(src="RL_Logo.png", height = 100, width = 100, alt = "R.Lum"), p("Links:"), a(href = "http://www.r-luminescence.de", "R.Luminescence project page", target="_blank"), br(), a(href = "https://forum.r-luminescence.de", "Message board", target="_blank"), br(), a(href = "http://zerk.canopus.uberspace.de/R.Lum", "Online application", target="_blank"), br(),hr(), img(src='GitHub-Mark-32px.png', width='32px', height='32px'), br(), a(href = "https://github.com/tzerk/RLumShiny/tree/master/inst/shiny/doserecovery", "See the code at GitHub!", target="_blank") )#/div )##EndOf::Tab_xy ) ), # Show a plot of the generated distribution mainPanel(width = 7, # insert css code inside of the generated HTML file: # allow open dropdown menus to reach over the container tags$head(tags$style(type="text/css",".tab-content {overflow: visible;}")), tags$head(includeCSS("www/style.css")), # divide output in separate tabs via tabsetPanel tabsetPanel( tabPanel("Plot", plotOutput(outputId = "main_plot", height = "400px")), tabPanel("Primary data set", fluidRow(column(width = 12, dataTableOutput("dataset")))), tabPanel("Secondary data set", dataTableOutput("dataset2")), tabPanel("R plot code", verbatimTextOutput("plotCode")) ) ) )RLumShiny/inst/shiny/doserecovery/server.R0000644000176200001440000002074212743662035020432 0ustar liggesusers## Server.R library(Luminescence) library(shiny) ## read example data set and misapply them for this plot type data(ExampleData.DeValues, envir = environment()) ExampleData.DeValues <- ExampleData.DeValues$BT998 ############################################################################## ### MAIN PROGRAM ### ############################################################################## shinyServer(function(input, output, session) { # check and read in file (DATA SET 1) datGet<- reactive({ inFile<- input$file1 if(is.null(inFile)) return(NULL) # if no file was uploaded return NULL return(read.table(file = inFile$datapath, # inFile[1] contains filepath sep = input$sep, quote = "", header = input$headers)) # else return file }) # check and read in file (DATA SET 2) datGet2<- reactive({ inFile2<- input$file2 if(is.null(inFile2)) return(NULL) # if no file was uploaded return NULL return(read.table(file = inFile2$datapath, # inFile[1] contains filepath sep = input$sep, quote = "", header = input$headers)) # else return file }) ### GET DATA SETS Data<- reactive({ if(!is.null(datGet())) { if(!is.null(datGet2())) { data<- list(datGet(), datGet2()) } else { data<- list(datGet()) } } else { x.1 <- ExampleData.DeValues[7:11,] x.2 <- ExampleData.DeValues[7:11,] * c(runif(5, 0.9, 1.1), 1) data<- list(x.1, x.2) } }) output$xlim<- renderUI({ data<- Data() n<- nrow(data[[1]]) sliderInput(inputId = "xlim", label = "Range x-axis", min = 0, max = n*2, value = c(1, n+1)) }) observe({ updateTextInput(session, inputId = "xlab", value = if(input$preheat==TRUE){"Preheat Temperature [\u00B0C]"}else{"# Aliquot"}) }) #### PLOT #### output$main_plot <- renderPlot({ input$refresh data<- Data() outputOptions(x = output, name = "xlim", suspendWhenHidden = FALSE) validate( need(expr = input$xlim, message = 'Waiting for data... Please wait!') ) # if custom datapoint style get char from separate input panel if(input$pch == "custom") { pch<- input$custompch } else { pch<- as.integer(input$pch)-1 #-1 offset in pch values } # if custom datapoint style get char from separate input panel if(input$pch2 == "custom") { pch2<- input$custompch2 } else { pch2<- as.integer(input$pch2)-1 #-1 offset in pch values } # if custom datapoint color get RGB code from separate input panel if(input$color == "custom") { color<- input$rgb } else { color<- input$color } if(length(data) > 1) { # if custom datapoint color get RGB code from separate input panel if(input$color2 == "custom") { color2<- input$rgb2 } else { color2<- input$color2 } } else { if(input$preheat == TRUE) { color2<- color } else { color2<- "white" } } if(length(data)==1){ given.dose<- input$dose legend<- input$legendname } else { given.dose<- c(input$dose, input$dose2) legend<- c(input$legendname, input$legendname2) } # save all arguments in a list args<- list(values = data, error.range = input$error, given.dose = given.dose, summary = input$stats, summary.pos = input$sumpos, boxplot = input$boxplot, legend = legend, legend.pos = input$legend.pos, main = input$main, mtext = input$mtext, col = c(color, color2), pch = c(pch, pch2), xlab = input$xlab, ylab = input$ylab, xlim = input$xlim, ylim = input$ylim, cex = input$cex) if(input$preheat == TRUE) { n<- length(data[[1]][,1]) ph<- c(input$ph1, input$ph2, input$ph3, input$ph4, input$ph5, input$ph6, input$ph7, input$ph8) ph<- ph[1:n] args<- c(args, "preheat" = NA) args$preheat<- ph args$pch<- rep(args$pch, n) args$col<- rep(args$col, n) } # plot DRT Results do.call(what = plot_DRTResults, args = args) # prepare code as text output if (is.null(input$sep)) updateRadioButtons(session, "fileformat", selected = "\t") if(input$sep == "\t") verb.sep<- "\\t" else verb.sep<- input$sep str1 <- paste("data <- read.delim(file, header = ",input$headers, ", sep= '", verb.sep,"')", sep = "") if(!is.null(datGet2())) { str2 <- "file2<- file.choose()" str3 <- paste("data2 <- read.delim(file2, header = ",input$headers, ", sep= '", verb.sep,"')", sep= "") str4 <- "data<- list(data, data2)" str1 <- paste(str1, str2, str3, str4, sep = "\n") } header <- paste("# To reproduce the plot in your local R environment", "# copy and run the following code to your R console.", "library(Luminescence)", "file<- file.choose()", str1, "\n", sep = "\n") names <- names(args) verb.arg <- paste(mapply(function(name, arg) { if (all(inherits(arg, "character"))) arg <- paste0("'", arg, "'") if (length(arg) > 1) arg <- paste0("c(", paste(arg, collapse = ", "), ")") if (is.null(arg)) arg <- "NULL" paste(name, "=", arg) }, names[-1], args[-1]), collapse = ",\n") funCall <- paste0("plot_DRTResults(values = data,\n", verb.arg, ")") code.output <- paste0(header, funCall, collapse = "\n") # nested renderText({}) for code output on "R plot code" tab output$plotCode<- renderText({ code.output })##EndOf::renderText({}) # nested downloadHandler() to print plot to file output$exportFile <- downloadHandler( filename = function() { paste(input$filename, ".", input$fileformat, sep="") }, content = function(file) { # determine desired fileformat and set arguments if(input$fileformat == "pdf") { pdf(file, width = input$imgwidth, height = input$imgheight, paper = "special", useDingbats = FALSE, family = input$fontfamily) } if(input$fileformat == "svg") { svg(file, width = input$imgwidth, height = input$imgheight, family = input$fontfamily) } if(input$fileformat == "eps") { postscript(file, width = input$imgwidth, height = input$imgheight, paper = "special", family = input$fontfamily) } # plot Abanico Plot do.call(what = plot_DRTResults, args = args) dev.off() },#EO content =, contentType = "image" )#EndOf::dowmloadHandler() }) # renderTable() that prints the data to the second tab output$dataset<- renderDataTable( options = list(pageLength = 10, autoWidth = FALSE), callback = "function(table) { table.on('click.dt', 'tr', function() { $(this).toggleClass('selected'); Shiny.onInputChange('rows', table.rows('.selected').data().toArray()); });}", { data<- Data() colnames(data[[1]])<- c("De", "De error") data[[1]] })##EndOf::renterTable() # renderTable() that prints the data to the second tab output$dataset2<- renderDataTable( options = list(pageLength = 10, autoWidth = FALSE), callback = "function(table) { table.on('click.dt', 'tr', function() { $(this).toggleClass('selected'); Shiny.onInputChange('rows', table.rows('.selected').data().toArray()); });}", { data<- Data() if(length(data)>1) { colnames(data[[2]])<- c("De", "De error") data[[2]] } })##EndOf::renterTable() }) RLumShiny/inst/shiny/doserecovery/www/0000755000176200001440000000000012743662035017620 5ustar liggesusersRLumShiny/inst/shiny/doserecovery/www/GitHub-Mark-32px.png0000644000176200001440000000326212743662035023175 0ustar liggesusersPNG  IHDR szztEXtSoftwareAdobe ImageReadyqe<$iTXtXML:com.adobe.xmp $IDATxėmhayL30A+R#f>IHکy(M)_o5 0+0Ėl&o{i^]u<{Yws}=uC>$L, }<w}8^ AO?p! xaяPKI3`'B>0QT1<+`}^nvkp^ƅF|1"Gp.*oO׀Vp ]߅jc8K$q 8jV`#`vmpGѢu!#}#:U_?_yhE $=;c*xNOo+&w)%K-R%6n'o">j/t³qoGW7j%2q GX?woibCÐAzbǰt \14|S.DZ]# b|H$(ʕohmqͱRP셣$,0Z20 tNvRW3K8Xk2 IO6F)X6of-/OK S, r RY~ApO|xˉN;@NZYJgnܟ) ߍz?\:qD/ Rz攟:})%8Cgo;ކ"Ғ͏JiYL!3czOϘiENr!/K(R "r옷lþ9nȉ'TxCP1N"9A]ՇW AANƗ}Ú.GJͥ:fx/kS//gtSusw)mo{[g|APS+z;~ѱߗ(ZU|%?{=vi! 5.^3 $v` uTAz(bs59$\{e3_dW_d S(9w{o[۶==v99!-@ x4X_?1_בr3B)@{r:M+ͤQTJEnXPckAEPS2NRJ5Q/ԶmYo/gT)(._qwi ǽѻadЋ\r !P-}1(*$yy !)R "a%_ +GPSh1!T/5ewR0[_=1_=N㼉!tpЛWZ+"S #w{_ ߼/nI6F9KڛhoחA0RD 5;Wo;qD;S?U)&$S-ȕ~eꎿ?9{N8#RzUYJ痟:obdr'*$_'<|9Gt $Wx^_PԆ5%e1=VNURLͯGK{ ^_<32!r YR }!}!"5Żmc?>㞿}R:WO9( i&}+I))=ϛuD/T _|5SQ@K!)EL 5l5sm ANRmAU/T j D!l \SR1[ .@P}L5АkAKǗUnX u?߻=_љ)+dBZYU2uԖ@~Q/eW_|=?~dݞ'Nhgd@}R*!,?u؛h Dɬ־usK;fx >zE=w2?)5HiFc`UP/T!AYxAEN]U)ݤ('TEP 洟?]?GN&[RB)fC?=FP 'D8KOӸm(R MA}OPBs#BAP;z!\h!,{*˱ci}?r qB(iRWv z dQ^ȜJ}BS@PB~^gu[;STJ+eR\GJ_qP#ˑSȳ{kHG>׎/+QqyN{%^[OzUP[*r bWӠ}R 7 o{w۶ǂ^DT5tWnS~갿 EHI)S=ϛuD%߲-j^)@KiHlkHBU%[W#-#)@k٧M)=okRZOP^-9ȷ]MDJGT)HT?" iB7;ez" "G֤U(-/_wǼ{eA}S OI D%ޒ[bj[BcVR3QSB]v%Ҷ<"YYIc7.텪TGPT } W#t˃E,[ʇ{JeAU/EƟ#}])EL&P/T ꭃLw*jUPS2)&F/56+#ٴo[l˹EP/T m~x% ^)@"?ncS\/2D%/GV_P#P;Y˛8ɥ/M\0}oKLmKZLz.ے7n[@ HJیS˛RX?c^he|\Ҏ^^oVS2h:#RZY0^(EAPWvTAˬ*r "d$AU5 u  ;H鱲nhNH+Ŗ\@@LYP HHґRh+*J,%A}Oz-PJkDNNǛHMYp,. 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iJM:I9Tژx?BR矯3")!*یYR%TWC@?GLQTA}IJ9?` LI>QB)HqUk %JY5b1.לJڃ-9>?l0 I!!sfC1IENDB`RLumShiny/inst/shiny/cosmicdose/0000755000176200001440000000000012743662035016413 5ustar liggesusersRLumShiny/inst/shiny/cosmicdose/ui.R0000644000176200001440000001671312743662035017163 0ustar liggesuserslibrary(RLumShiny) shinyUI(fluidPage( includeCSS("./www/style.css"), fluidRow( column(width = 3, div(align = "center", span(class="label label-info", "Site")), wellPanel( numericInput(inputId = "altitude", label = p(class="h","Altitude (m asl)"), value = 124, step = 1), tooltip(refId = "altitude", text = "Altitude (m above sea-level)"), selectInput(inputId = "coords", label = "Coordinates", selected = "decDeg", choices = c("Decimal degrees" = "decDeg", "Degrees decimal minutes" = "degDecMin", "Degrees minutes seconds" = "degMinSec")), conditionalPanel(condition = "input.coords == 'decDeg'", numericInput(inputId = "decDegN", label = p(class="h","North"), value = 50.926903, step = 0.000001), numericInput(inputId = "decDegE", label = p(class="h","East"), value = 6.937453, step = 0.000001) ), conditionalPanel(condition = "input.coords == 'degDecMin'", fluidRow( column(width = 4, numericInput(inputId = "degN_1", label = p(class="h","N: \uB0"), value = 50, step = 1), numericInput(inputId = "degE_1", label = p(class="h","E: \uB0"), value = 6, step = 1) ), column(width = 4, offset = 2, numericInput(inputId = "decMinN", label = p(class="h","Decimal \u27"), value = 55.61417, step = 0.000001), numericInput(inputId = "decMinE", label = p(class="h","Decimal \u27"), value = 56.24717, step = 0.000001) ) ) ), conditionalPanel(condition = "input.coords == 'degMinSec'", fluidRow( column(width = 3, offset = 0, numericInput(inputId = "degN_2", label = p(class="h","N: \uB0"), value = 50, step = 1), numericInput(inputId = "degE_2", label = p(class="h","E: \uB0"), value = 6, step = 1) ), column(width = 3, offset = 1, numericInput(inputId = "minN", label = p(class="h","\u27"), value = 55, step = 1), numericInput(inputId = "minE", label = p(class="h","\u27"), value = 56, step = 1) ), column(width = 3, offset = 1, numericInput(inputId = "secN", label = p(class="h","\u27\u27"), value = 36.85, step = 0.01), numericInput(inputId = "secE", label = p(class="h","\u27\u27"), value = 14.83, step = 0.01) ) ) ) ) ), column(width = 3, div(align = "center", span(class="label label-info", "Sediment")), wellPanel( numericInput(inputId = "density_1", label = p(class="h","Density (g/cm\uB3)"), value = 2.0, step = 0.1), tooltip(refId = "density_1", text = "Average overburden density (g/cm\uB3)."), conditionalPanel(condition = "input.mode == 'xAsS'", numericInput(inputId = "density_2", label = p(class="h","Density (g/cm\uB3)"), value = NULL, step = 0.1), numericInput(inputId = "density_3", label = p(class="h","Density (g/cm\uB3)"), value = NULL, step = 0.1), numericInput(inputId = "density_4", label = p(class="h","Density (g/cm\uB3)"), value = NULL, step = 0.1), numericInput(inputId = "density_5", label = p(class="h","Density (g/cm\uB3)"), value = NULL, step = 0.1) ) ) ), column(width = 3, div(align = "center", span(class="label label-info", "Samples")), wellPanel( numericInput(inputId = "depth_1", label = p(class="h","Depth (m)"), value = 1.00, step = 0.01), tooltip("depth_1", text = "Depth of overburden (m)."), conditionalPanel(condition = "input.mode == 'sAxS' || input.mode == 'xAsS'", numericInput(inputId = "depth_2", label = p(class="h","Depth (m)"), value = NULL, step = 0.01), numericInput(inputId = "depth_3", label = p(class="h","Depth (m)"), value = NULL, step = 0.01), numericInput(inputId = "depth_4", label = p(class="h","Depth (m)"), value = NULL, step = 0.01), numericInput(inputId = "depth_5", label = p(class="h","Depth (m)"), value = NULL, step = 0.01) ) ) ), column(width = 3, div(align = "center", span(class="label label-info", "Options")), wellPanel( checkboxInput(inputId = "corr", label = p(class="h","Correct for geomagnetic field changes"), value = FALSE), tooltip(refId = "corr", text = "Correct for geomagnetic field changes after Prescott & Hutton (1994). Apply only when justified by the data."), numericInput(inputId = "estage", label = p(class="h","Estimated age"), value = 30, step = 1, min = 0, max = 80), tooltip(refId = "estage", text = "Estimated age range (ka) for geomagnetic field change correction (0-80 ka allowed)."), checkboxInput(inputId = "half", label = p(class="h","Use half the depth"), value = FALSE), tooltip(refId = "half", text = " How to overcome with varying overburden thickness. If TRUE only half the depth is used for calculation. Apply only when justified, i.e. when a constant sedimentation rate can safely be assumed."), numericInput(inputId = "error", label = p(class="h","General error (%)"), value = 10, step = 1), tooltip(refId = "error", text = "General error (percentage) to be implemented on corrected cosmic dose rate estimate"), selectInput(inputId = "mode", label = "Mode", selected = "sAsS", choices = c("1 absorber, 1 sample" = "sAsS", "x absorber, 1 sample" = "xAsS", "1 absorber, x samples" = "sAxS")) ), actionButton(inputId = "refresh", label = "", icon = icon("refresh")), tooltip(refId = "refresh", text = "Reload app") ) ), fluidRow( column(width = 6, div(id="gmap", htmlOutput("map") ) ), column(width = 6, div(align = "center", h6("Results")), conditionalPanel(condition = "input.mode == 'sAsS' || input.mode == 'xAsS'", wellPanel( htmlOutput("results") )), conditionalPanel(condition = "input.mode == 'sAxS'", dataTableOutput("resultsTable") ) ) ), includeCSS("./www/style.css") ))RLumShiny/inst/shiny/cosmicdose/server.R0000644000176200001440000001074112743662035020047 0ustar liggesusers## Server.R library(Luminescence) library(shiny) library(googleVis) ## MAIN FUNCTION shinyServer(function(input, output, session) { # function to convert coordinates to degree decimal format coord_conv<- function(x, id) { if(id=="degDecMin") { x<- paste(as.character(sum(input$degN_1, input$decMinN/60)),":", as.character(sum(input$degE_1, input$decMinE/60)), sep = "") } if(id=="degMinSec") { x<- paste(as.character(sum(input$degN_2,input$minN/60,input$secN/3600)),":", as.character(sum(input$degE_2,input$minE/60,input$secE/3600)), sep = "") } return(x) } # coordinate conversion coords<- reactive({ if(input$coords != "decDeg") { LatLong<- ifelse(input$coords=="degDecMin", coord_conv(, id="degDecMin"), # YES coord_conv(, id ="degMinSec")) # NO } else { LatLong<- paste(input$decDegN,":",input$decDegE,sep="") } # return data frame d<- data.frame(LatLong = LatLong, tip = "Site") return(d) }) # googleVis Map options myOptionsMap<- reactive({ opt<- list(enableScrollWheel = TRUE, showTip = TRUE, useMapTypeControl = TRUE, mapType = "terrain") return(opt) }) # render googleVis map output$map<- renderGvis({ # refresh plot on button press input$refresh gvisMap(data = coords(), locationvar = "LatLong", tipvar = "tip", options = myOptionsMap()) }) # get results from calc_CosmicDoseRate() function get_results<- reactive({ # get coordinates coords<- as.vector(coords()$LatLong) lat<- as.numeric(unlist(strsplit(x = coords, split = ":"))[1]) long<- as.numeric(unlist(strsplit(x = coords, split = ":"))[2]) # get absorber properties depth<- na.omit(c(input$depth_1, input$depth_2, input$depth_3, input$depth_4, input$depth_5)) density<- na.omit(c(input$density_1, input$density_2, input$density_3, input$density_4, input$density_5)) t<- get_RLum(calc_CosmicDoseRate(depth = depth, density = density, latitude = lat, longitude = long, altitude = input$altitude, corr.fieldChanges = input$corr, est.age = input$estage, half.depth = input$half, error = input$error), "summary") return(t) }) # render results for mode 1 and 2 output$results<- renderUI({ # refresh plot on button press input$refresh if(input$mode == "sAsS" || input$mode == "xAsS") { t<- get_results() HTML( if(input$mode=="xAsS") { paste("Sample depth: ","", "", sum(na.omit(input$depth_1), na.omit(input$depth_2), na.omit(input$depth_3), na.omit(input$depth_4), na.omit(input$depth_5)), "m", "", "", "
") }, "Total absorber: ","", "", t$total_absorber.gcm2, "g/cm\u00b2", "", "", "
", "Cosmic dose rate (uncorrected): ","", "", round(t$d0, 3), "Gy/ka", "", "", "
", "Geomagnetic latitude: ","", "", round(t$geom_lat, 2), "\u00b0", "", "", "
", "Cosmic dose rate (corrected): ","", "", round(t$dc, 3),"\u00b1", round(t$dc/100*input$error, 3), "Gy/ka", "", "
", "" ) } }) # render results for mode 3 output$resultsTable<- renderDataTable({ # refresh plot on button press input$refresh if(input$mode == "sAxS") { t<- get_results() table<- as.data.frame(cbind(t$depth, t$total_absorber.gcm2, round(t$d0, 3), round(t$dc,3), round(t$dc/100*input$error, 3))) colnames(table)<- c("Depth (m)", "Absorber (g/cm\u00b2)", "Dc (Gy/ka) [uncorrected]", "Dc (Gy/ka) [corrected]", "Dc error (Gy/ka)") table } }, options=list(autoWidth = FALSE, paging = FALSE, processing = TRUE)) # jQuery DataTables options (http://datatables.net) })RLumShiny/inst/shiny/cosmicdose/www/0000755000176200001440000000000012743662035017237 5ustar liggesusersRLumShiny/inst/shiny/cosmicdose/www/RL_Logo_alpha.png0000644000176200001440000003514612743662035022420 0ustar liggesusersPNG  IHDRYgAMA|Q cHRMz%u0`:o_FPLTE "000222;;;6GgOOOkkkK`aodpmzayv6YtRNSS% pHYs."."ݒtEXtSoftwarepaint.net 4.0.3P5IDATx^v#G]a-,nK  .@Z;bOTUdD q@&/dPm=5mؼ>=1mJw(i<=m=MmּO3Y>& %b2ک-U<#l簗;yyKH{vG4qH![10pC[sʉ(62`^Aj!@[yټƼmŽ!dFH:(Ž!bPCށaGWyǼDy+ؼo` ~]B;y+ؼc0|bGWyՓeMy+׼͛#y4}k^Mq]ByּL2hCv4q՚Wy̛'y4}k^O >';bͫ;{ڔC\սyڕC\&KC_Wv̛饼WڗC\z)vfGWyEǼٮk_hkv4qWs̛1y4}j^1oy4}ѼOC_%W~ɣyDJyGW敺EhмJcO_nh*4O?4IC_Wi]kkGGޛ>~h+F7:;8גĎ!浤#yk=m֎!B qdՎ!Bj z-M^hJ4̳:DO[y+ѼZ^iv4q4hhYGO۴y+ҼZL=Ҏ!H zGOyҼOdhv4qUWoЛ14Ў!Ljݗ|4oA;2ͫ8yzڟC\UgGWy%Y<j^Aoisv4qWsЛF=͎!Rjz6ᧈjkv4qWtЛm̎!Tz}<ĕj^Aoi[v4qWvЛ ʎ!Vz}6eGWy>Go%;b+1i+v4qWd zډC\&?Yyؼ~6hJ6/P=Ž!d;+6ƋZhj6oAoQOy+ڼQ7zZC\ 6ƫAG=ގ!jFx;+R8iv4qe7!z=\`4q4,Ƽ}<Ѽsxl'4q4Ƽ<Ѽ3BG` CvCGb C!}ACG>#y;yy<Ӽ<ѼOHޞhhG|hhGyyyپhhyyyhh{y;yy0!Ø78!潡yyy?TI޿_ C;!y/=ehhI1d<<ʴw;{4q4Oy|0MhhQ20Ņ.C;2[`<ѼWU:<3phhޫAƼw C{1Ԙpyy/yZ:=PhhAۑW#|4q4HIxhhcuvih^N<Ѽ2c٧6B4q4Sg[)>87wF}4qg{OԎ!}y˟:ۂC\ك]h7ʘ<5ot#/okGGJrlmhz7GW=i=y4}n^1桯͛nwyܼ*c}g;ّC\5hۼO{<ղyKC_-WeKZNZC\1}%<<:;CkyyyghMv4q71-ʎ!nU\&Ў!nUJ>uvZCc̻mG7vy|hv4qC7< ݼ*c3-܎!nq;ݴr;88-g$ZCc̻nG7nxZCܸc{nG7l< ۼ*chOiv4q6<čڼ*cpOiv4q6< <Ƽhv4qc61AZCܘͫ2i9hl#?Jyy7y4}<Ƽiv4q6-< ؼ*cޘOi v4q5~|Fhyyhk.mŽ!nUF}Hyy\`WڝC\U{Hy+<:ۗgGWyyhj61ogڟC\U&|Hy+<:ۛ6hGWyU<-gBڠC\q;C;8w3#Ў!`-\Ay+׼*cެOiv4q՚SgڥC\1Yhv4qŚSgڦC\Up6hj51Dyռ*c3/ӎ!TEyy_͟<*51F;y+<:Vh 51G[yӼH<4ʘ7SgGګC\NڬC\UfHy<:nh41Jy+<*aej1步yxy7E,yxy[7CV<<ؼ_֛y$o={Sh^K::; z7AggGE|gfĢni),|ni-d`tk>@ۺy-E lHC 'h`P^ȓ󛟴 pX``gU;4@*R+"whuͻ H3Q5 B.@ $pd!s#~<<+"x M0B\t8K@zB@F&S`cbP-`'{[! eDh;VEX0fK9-0IWfH  0Q){`##xFW<+*x<$9E[-qWW.(I+6aa@.y24x6_-"bbϫp@t~,/;m%h^ uf@Wp~<5j>{-]cK'Xto(hw?G%fIq^D$.Tʳ?D*A, `6B$BB dr`)B(Ͱ*`/@4Qhp.U=pa( Aa!ڈbX#!H$ ɈQ"K5H1RT UH=r9\F;2G1Q= C7F dt1r=6Ыhڏ>C03l0.B8, c˱" VcϱwE 6wB aAHXLXNH $4 7 Q'"K&b21XH,#/{C7$C2'ITFnR#,4H#dk9, +ȅ3![ b@qS(RjJ4e2AURݨT5ZBRQ4u9̓IKhhitݕNWGw Ljg(gwLӋT071oUX**| J&*/Tު UUT^S}FU3S ԖUPSSg;goT?~YYLOCQ_ cx,!k u5&|v*=9C3J3WRf?qtN (~))4L1e\kXHQG6EYAJ'\'GgSSݧ M=:.kDwn^Loy}/TmG X $ <5qo</QC]@Caaᄑ.ȽJtq]zۯ6iܟ4)Y3sCQ? 0k߬~OCOg#/c/Wװwa>>r><72Y_7ȷOo_C#dz%gA[z|!?:eAAA!h쐭!ΑiP~aa~ 'W?pX15wCsDDDޛg1O9-J5*>.j<74?.fYXXIlK9.*6nl {/]py.,:@LN8A*%w% yg"/6шC\*NH*Mz쑼5y$3,幄'L Lݛ:v m2=:1qB!Mggfvˬen/kY- BTZ(*geWf͉9+̳ې7ᒶKW-X潬j9(xoʿܔĹdff-[n ڴ VE/(ۻCɾUUMfeI?m]Nmq#׹=TR+Gw- 6 U#pDy  :v{vg/jBFS[b[O>zG499?rCd&ˮ/~јѡ򗓿m|x31^VwwO| (hSЧc3-gAMA|Q cHRMz%u0`:o_FiIDATx}td%! )+7ږJ["\wKIQl7YWtFuftZǙ]=8n-Ot) q\p7ab SZMM@z K[yӧO?_7n\ pw~ \i$eo .<_: @IpB^D=c,JN+߻jժ8|()ٞ /MMM#g̙d\]w5f߾}}vP2.^zTq㢯ψ˼W馛FGN#P.NȦG"suhll4(E%>F]]Q~o=6mdPcbŊZ|ب˼xaPl."o,۷o7.E˼۷… K;|XRJw}~(T_u^^矏F?mƼ|>{WkΜ9 sl瞲^O$y1qIJƍ>?qZ*/,YR߳?8F-uy۷o VOF8GrWXQIU\VZ~OVײo߾ؾ}>F$yӧW4nܸ2oΜ9U5GN? 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padding-top: 10px; padding-bottom: 10px; padding-right: 10px; line-height: 200%; background-color: #fff; overflow: visible; position: absolute; z-index: 999; border-radius: 10px; border-style: solid; border-color: #428bca; } .h { font-size: 11px; margin: 0 0 0px; } h5 { color: #428bca; font-family:"Lucida Console", Monaco, monospace; font-weight: 700; } h6 { font-size: 16px; color: #428bca; font-family:"Lucida Console", Monaco, monospace; } .tooltip-inner { max-width: 450px; } #gmap { border-style: solid; border-width: 2px; border-color: #428bca; margin-top: 40px; } .control-label, .selectize-dropdown, .item, .uneditable-input, .sorting, .odd, .even, .dataTables-info, .fa, .fa-refresh { font-size: 11px; } .selectize-input { padding: 0px 10px; min-height: 20px; } .label, .badge { font-size: 14px; padding: 4px 20px; margin: 10px; line-height: 36px; font-weight: 100 !important; } .label-info, .badge-info { background-color: #428bca; } input[type="text"],input[type="number"],input[type="email"],input[type="url"],input[type="search"],input[type="tel"],input[type="color"],.uneditable-input{ display:inline-block; height:18px; padding:0px 0px 0px 7px; margin-bottom:10px; font-size: 11px; line-height: 1.5; color:#555; vertical-align:middle; -webkit-border-radius:4px; -moz-border-radius:4px; border-radius:4px } input,textarea,.uneditable-input{ width: auto; } .well { padding: 5px 19px; } RLumShiny/inst/shiny/KDE/0000755000176200001440000000000012743662035014666 5ustar liggesusersRLumShiny/inst/shiny/KDE/ui.R0000644000176200001440000005124112743662035015431 0ustar liggesuserslibrary(RLumShiny) ## UI.R # load example data data(ExampleData.DeValues) # pageWithSidebar contains three panels: # 1 - headerPanel: basically just for a header # 2 - sidebarPanel: data input # 3 - mainPanel: data output pageWithSidebar( # 1 - title = NULL -> Panel will not be shown headerPanel(title = NULL), # 2- width = 5 -> refers to twitters bootstrap grid system # where the the maximum width is 12 that is to be shared between all # elements sidebarPanel(width = 5, # include a tabs in the input panel for easier navigation tabsetPanel(id = "tabs", type = "pill", selected = "Data", # Tab 1: Data input tabPanel("Data", # informational text div(align = "center", h5("Data upload")), # file upload button (data set 1) fileInput(inputId = "file1", label = strong("Primary data set"), accept="text/plain"), tooltip(refId = "file1", text = tags$img(src='file_structure.png', width='250px')), # file upload button (data set 2) fileInput(inputId = "file2", label = strong("Secondary data set"), accept="text/plain"), tooltip(refId = "file2", text = tags$img(src='file_structure.png', width='250px')), # informational text div(align = "center", h5("Settings")), fluidRow( column(width = 6, # logical: should NA values be excluded? checkboxInput(inputId = "naExclude", label = "Exclude NA values", value = TRUE), tooltip(refId = "naExclude", text = "Exclude NA values from the data set prior to any further operations.") ), column(width = 6, # logical: file contains headers? checkboxInput(inputId = "headers", label = "File contains headers", value = FALSE), tooltip(refId = "headers", text = tags$img(src='file_containsHeader.png', width='250px')) )), # char: columns separated by tab, space, comma radioButtons("sep", "Separator", selected = "\t", inline = TRUE, c("Tab" = "\t", "Space" = " ", "Comma" = ",", "Semicolon" = ";")), tooltip(refId = "sep", text = tags$img(src='file_sep.png', width='400px'), placement = "auto left"), hr(), actionButton(inputId = "refresh", label = "Refresh", icon = icon("refresh")), tooltip(refId = "refresh", text = "Redraw the plot") ),##EndOf::Tab_1 # Tab 2: Statistical information tabPanel("Statistics", div(align = "center", h5("Summary")), fluidRow( column(width = 6, checkboxInput(inputId = "summary", label = "Show summary", value = FALSE), tooltip(refId = "summary", text = "Adds numerical output to the plot") ), column(width = 6, selectInput(inputId = "sumpos", label = "Summary position", selected = "topleft", choices = list("Subtitle" = "sub", "Center" = "center", Top=c("Top" = "top", "Top left" = "topleft", "Top right"= "topright"), Bottom=c("Bottom" = "bottom", "Bottom left" = "bottomleft", "Bottom right" = "bottomright") )), tooltip(refId = "sumpos", attr = "for", text = "Position of the statistical summary. The keyword \"Subtitle\" will only work if no plot subtitle is used.") ) ), selectInput(inputId = "summary.method", label = "Summary method", selected = "unweighted", choices = list("Unweighted" = "unweighted", "Weighted" = "weighted", "Monte Carlo" = "MCM")), tooltip(refId = "summary.method", attr = "for", text = "Keyword indicating the method used to calculate the statistic summary. See calc_Statistics for details."), checkboxGroupInput(inputId = "stats", label = "Parameters", selected = c("n","mean"), choices = c("n" = "n", "Mean" = "mean", "Median" = "median", "rel. Standard deviation" = "sd.rel", "abs. Standard deviation" = "sd.abs", "rel. Standard error" = "se.rel", "abs. Standard error" = "se.abs", "Skewness" = "skewness", "Kurtosis" = "kurtosis", "% in 2 sigma range" = "in.2s")), tooltip(refId = "stats", text = "Statistical parameters to be shown in the summary"), div(align = "center", h5("Additional options")), checkboxInput(inputId = "cumulative", label = "Show individual data", value = TRUE), tooltip(refId = "cumulative", text = "Show cumulative individual data.") ),##EndOf::Tab_2 # Tab 3: input that refer to the plot rather than the data tabPanel("Plot", div(align = "center", h5("Title")), textInput(inputId = "main", label = "Title", value = "KDE Plot"), # inject sliderInput from Server.R uiOutput(outputId = "bw"), tooltip(refId = "bw", text = "Bin width of the kernel density estimate"), br(), div(align = "center", h5("Scaling")), sliderInput(inputId = "cex", label = "Scaling factor", min = 0.5, max = 2, value = 1.0, step = 0.1), div(align = "center", h5("Further options")), fluidRow( column(width = 6, checkboxInput(inputId = "rug", label = "Add rug", value = TRUE) ), column(width = 6, checkboxInput(inputId = "boxplot", label = "Add boxplot", value = TRUE)) ) ),##EndOf::Tab_3 # Tab 4: modify axis parameters tabPanel("Axis", div(align = "center", h5("X-axis")), checkboxInput(inputId = "logx", label = "Logarithmic x-axis", value = FALSE), textInput(inputId = "xlab", label = "Label x-axis", value = "Equivalent dose [Gy]"), # inject sliderInput from Server.R uiOutput(outputId = "xlim"), br(), div(align = "center", h5("Y-axis")), fluidRow( column(width = 6, textInput(inputId = "ylab1", label = "Label y-axis (left)", value = "Density") ), column(width = 6, textInput(inputId = "ylab2", label = "Label y-axis (right)", value = "Cumulative frequency") ) ) ),##EndOf::Tab_4 # Tab 5: modify data point representation tabPanel("Datapoints", div(align = "center", h5("Primary data set")), fluidRow( column(width = 6, selectInput(inputId = "color", label = "Datapoint color", choices = list("Black" = "black", "Grey" = "grey50", "Red" = "#b22222", "Green" = "#6E8B3D", "Blue" = "#428bca", "Custom" = "custom")) ), column(width = 6, # show only if custom color is desired conditionalPanel(condition = "input.color == 'custom'", jscolorInput(inputId = "rgb", label = "Choose a color")) ) ), div(align = "center", h5("Secondary data set")), fluidRow( column(width = 6, selectInput(inputId = "color2", label = "Datapoint color", selected = "#b22222", choices = list("Black" = "black", "Grey" = "grey50", "Red" = "#b22222", "Green" = "#6E8B3D", "Blue" = "#428bca", "Custom" = "custom")) ), column(width = 6, # show only if custom color is desired conditionalPanel(condition = "input.color2 == 'custom'", jscolorInput(inputId = "rgb2", label = "Choose a color")) ) ) ),##EndOf::Tab_5 # Tab 9: save plot as pdf, wmf or eps tabPanel("Export", radioButtons(inputId = "fileformat", label = "Fileformat", choices = c("PDF (Portable Document Format)" = "pdf", "SVG (Scalable Vector Graphics)" = "svg", "EPS (Encapsulated Postscript)" = "eps")), textInput(inputId = "filename", label = "Filename", value = "KDE Plot"), fluidRow( column(width = 6, numericInput(inputId = "imgheight", label = "Image height", value = 7) ), column(width = 6, numericInput(inputId = "imgwidth", label = "Image width", value = 7) ) ), selectInput(inputId = "fontfamily", label = "Font", selected = "Helvetica", choices = c("Helvetica" = "Helvetica", "Helvetica Narrow" = "Helvetica Narrow", "Times" = "Times", "Courier" = "Courier", "Bookman" = "Bookman", "Palatino" = "Palatino")), tags$hr(), downloadButton(outputId = "exportFile", label = "Download plot"), tags$hr(), helpText("Additionally, you can download a corresponding .R file that contains", "a fully functional script to reproduce the plot in your R environment!"), downloadButton(outputId = "exportScript", label = "Download R script") ),##EndOf::Tab_8 # Tab 10: further information tabPanel("About", hr(), div(align = "center", # HTML code to include a .png file in the tab; the image file must be in # a subfolder called "wwww" img(src="RL_Logo.png", height = 100, width = 100, alt = "R.Lum"), p("Links:"), a(href = "http://www.r-luminescence.de", "R.Luminescence project page", target="_blank"), br(), a(href = "https://forum.r-luminescence.de", "Message board", target="_blank"), br(), a(href = "http://zerk.canopus.uberspace.de/R.Lum", "Online application", target="_blank"), br(),hr(), img(src='GitHub-Mark-32px.png', width='32px', height='32px'), br(), a(href = "https://github.com/tzerk/RLumShiny/tree/master/inst/shiny/KDE", "See the code at GitHub!", target="_blank") )#/div )##EndOf::Tab_9 )##EndOf::tabsetPanel ),##EndOf::sidebarPanel # 3 - output panel mainPanel(width = 7, # insert css code inside of the generated HTML file: # allow open dropdown menus to reach over the container tags$head(tags$style(type="text/css",".tab-content {overflow: visible;}")), tags$head(includeCSS("www/style.css")), # divide output in separate tabs via tabsetPanel tabsetPanel( tabPanel("Plot", plotOutput(outputId = "main_plot", height = "500px")), tabPanel("Primary data set", dataTableOutput("dataset")), tabPanel("Secondary data set", dataTableOutput("dataset2")), tabPanel("Central Age Model", dataTableOutput("CAM")), tabPanel("R plot code", verbatimTextOutput("plotCode")) )###EndOf::tabsetPanel )##EndOf::mainPanel )##EndOf::shinyUI(pageWithSidebar)RLumShiny/inst/shiny/KDE/server.R0000644000176200001440000002743112743662035016326 0ustar liggesusers## Server.R library(Luminescence) library(shiny) # load example data data(ExampleData.DeValues) data <- list(ExampleData.DeValues$CA1, ExampleData.DeValues$CA1) ## MAIN FUNCTION shinyServer(function(input, output, session) { # check and read in file (DATA SET 1) datGet<- reactive({ inFile<- input$file1 if(is.null(inFile)) return(NULL) # if no file was uploaded return NULL return(read.table(file = inFile$datapath, # inFile[1] contains filepath sep = input$sep, quote = "", header = input$headers)) # else return file }) # check and read in file (DATA SET 2) datGet2<- reactive({ inFile2<- input$file2 if(is.null(inFile2)) return(NULL) # if no file was uploaded return NULL return(read.table(file = inFile2$datapath, # inFile[1] contains filepath sep = input$sep, quote = "", header = input$headers)) # else return file }) # dynamically inject sliderInput for x-axis range output$xlim<- renderUI({ # check if file is loaded # # case 1: yes -> slinderInput with custom values if(!is.null(datGet())) { if(!is.null(datGet2())) { data<- rbind(datGet(),datGet2()) sliderInput(inputId = "xlim", label = "Range x-axis", min = min(data[,1])*0.25, max = max(data[,1])*1.75, value = c(min(data[,1])*0.9, max(data[,1])*1.1)) } else { data<- datGet() sliderInput(inputId = "xlim", label = "Range x-axis", min = min(data[,1])*0.25, max = max(data[,1])*1.75, value = c(min(data[,1])*0.9, max(data[,1])*1.1)) } } else { #case 2: no -> sliderInput for example data sliderInput(inputId = "xlim", label = "Range x-axis", min = min(data[[1]][,1])*0.25, max = max(data[[1]][,1])*1.75, value = c(min(data[[1]][,1])*0.9, max(data[[1]][,1]))*1.05, step = 1, round = 0) } })## EndOf::renderUI() # dynamically inject sliderInput for KDE bandwidth output$bw<- renderUI({ # check if file is loaded # # case 1: yes -> slinderInput with custom values if(!is.null(datGet())) { if(!is.null(datGet2())) { data<- rbind(datGet(),datGet2()) sliderInput(inputId = "bw", label = "KDE bandwidth", min = bw.nrd0(data[,1])/4, max = bw.nrd0(data[,1])*4, value = bw.nrd0(data[,1])) } else { data<- datGet() sliderInput(inputId = "bw", label = "KDE bandwidth", min = bw.nrd0(data[,1])/4, max = bw.nrd0(data[,1])*4, value = bw.nrd0(data[,1])) } } else { #case 2: no -> sliderInput for example data # logged data sliderInput(inputId = "bw", label = "KDE bandwidth", min = 1, max = 100, value = 15, step = 1) } })## EndOf::renderUI() output$main_plot <- renderPlot({ # refresh plot on button press input$refresh # progress bar progress<- Progress$new(session, min = 0, max = 3) progress$set(message = "Calculation in progress", detail = "Retrieve data") on.exit(progress$close()) # make sure that input panels are registered on non-active tabs. # by default tabs are suspended and input variables are hence # not available outputOptions(x = output, name = "xlim", suspendWhenHidden = FALSE) outputOptions(x = output, name = "bw", suspendWhenHidden = FALSE) # check if file is loaded and overwrite example data if(!is.null(datGet())) { data<- list(datGet(), datGet()) } if(!is.null(datGet2())) { data2<- datGet2() } if(is.null(datGet()) == FALSE && is.null(datGet2()) == FALSE) { data<- datGet() data2<- datGet2() data<- list(data, data2) } progress$set(value = 1) progress$set(message = "Calculation in progress", detail = "Get values") # check if any summary stats are activated, else NA if (input$summary) { summary<- input$stats } else { summary<- "" } if(input$logx == TRUE) { logx<- "x" } else { logx<- "" } # update progress bar progress$set(value = 2) progress$set(message = "Calculation in progress", detail = "Combine values") # if custom datapoint color get RGB code from separate input panel if(input$color == "custom") { color<- input$rgb } else { color<- input$color } if(!is.null(datGet2())) { # if custom datapoint color get RGB code from separate input panel if(input$color2 == "custom") { color2<- input$rgb2 } else { color2<- input$color2 } } else { color2<- adjustcolor("white", alpha.f = 0) } # validate(need()) makes sure that all data are available to # renderUI({}) before plotting and will wait until there validate( need(expr = input$xlim, message = 'Waiting for data... Please wait!'), need(expr = input$bw, message = 'Waiting for data... Please wait!') ) progress$set(value = 3) progress$set(message = "Calculation in progress", detail = "Ready to plot") args <- list(data = data, cex = input$cex, log = logx, xlab = input$xlab, ylab = c(input$ylab1, input$ylab2), main = input$main, values.cumulative = input$cumulative, na.rm = input$naExclude, rug = input$rug, boxplot = input$boxplot, summary = summary, summary.pos = input$sumpos, summary.method = input$summary.method, bw = input$bw, xlim = input$xlim, col = c(color, color2)) do.call(plot_KDE, args = args) # prepare code as text output if (is.null(input$sep)) updateRadioButtons(session, "fileformat", selected = "\t") if(input$sep == "\t") verb.sep<- "\\t" else verb.sep<- input$sep str1 <- paste("data <- read.delim(file, header = ",input$headers, ", sep= '", verb.sep,"')", sep = "") if(!is.null(datGet2())) { str2 <- "file2<- file.choose()" str3 <- paste("data2 <- read.delim(file2, header = ",input$headers, ", sep= '", verb.sep,"')", sep= "") str4 <- "data<- list(data, data2)" str1 <- paste(str1, str2, str3, str4, sep = "\n") } header <- paste("# To reproduce the plot in your local R environment", "# copy and run the following code to your R console.", "library(Luminescence)", "file<- file.choose()", str1, "\n", sep = "\n") names <- names(args) verb.arg <- paste(mapply(function(name, arg) { if (all(inherits(arg, "character"))) arg <- paste0("'", arg, "'") if (length(arg) > 1) arg <- paste0("c(", paste(arg, collapse = ", "), ")") if (is.null(arg)) arg <- "NULL" paste(name, "=", arg) }, names[-1], args[-1]), collapse = ",\n") funCall <- paste0("plot_KDE(data = data,\n", verb.arg, ")") code.output <- paste0(header, funCall, collapse = "\n") # nested renderText({}) for code output on "R plot code" tab output$plotCode<- renderText({ code.output })##EndOf::renderText({}) output$exportScript <- downloadHandler( filename = function() { paste(input$filename, ".", "R", sep="") }, content = function(file) { write(code.output, file) },#EO content =, contentType = "text" )#EndOf::dowmloadHandler() # nested downloadHandler() to print plot to file output$exportFile <- downloadHandler( filename = function() { paste(input$filename, ".", input$fileformat, sep="") }, content = function(file) { if(is.null(input$fileformat)) updateRadioButtons(session, inputId = "fileformat", label = "Fileformat", selected = "pdf") # determine desired fileformat and set arguments if(input$fileformat == "pdf") { pdf(file, width = input$imgwidth, height = input$imgheight, paper = "special", useDingbats = FALSE, family = input$fontfamily) } if(input$fileformat == "svg") { svg(file, width = input$imgwidth, height = input$imgheight, family = input$fontfamily) } if(input$fileformat == "eps") { postscript(file, width = input$imgwidth, height = input$imgheight, paper = "special", family = input$fontfamily) } do.call(plot_KDE, args = args) dev.off() },#EO content =, contentType = "image" )#EndOf::dowmloadHandler() })##EndOf::renderPlot({}) # renderTable() that prints the data to the second tab output$dataset<- renderDataTable( options = list(pageLength = 10, autoWidth = FALSE), callback = "function(table) { table.on('click.dt', 'tr', function() { $(this).toggleClass('selected'); Shiny.onInputChange('rows', table.rows('.selected').data().toArray()); }); }", { if(!is.null(datGet())) { data<- datGet() colnames(data)<- c("De","De error") data } else { data<- data[[1]] colnames(data)<- c("De","De error") data } })##EndOf::renterTable() # renderTable() that prints the secondary data to the second tab output$dataset2<- renderDataTable( options = list(pageLength = 10, autoWidth = FALSE), callback = "function(table) { table.on('click.dt', 'tr', function() { $(this).toggleClass('selected'); Shiny.onInputChange('rows', table.rows('.selected').data().toArray()); }); }", { if(!is.null(datGet2())) { data<- datGet2() colnames(data)<- c("De","De error") data } else { } })##EndOf::renterTable() # renderTable() to print the results of the # central age model (CAM) output$CAM<- renderDataTable( options = list(pageLength = 10, autoWidth = FALSE), { if(!is.null(datGet())) { if(!is.null(datGet2())) { data<- list(datGet(), datGet2()) } else { data<- list(datGet()) } } else { data<- list(data[[1]]) } t<- as.data.frame(matrix(nrow = length(data), ncol = 7)) colnames(t)<- c("Data set","n", "log data", "Central dose", "SE abs.", "OD (%)", "OD error (%)") res<- lapply(data, function(x) { calc_CentralDose(x, verbose = FALSE, plot = FALSE) }) for(i in 1:length(res)) { t[i,1]<- ifelse(i==1,"pimary","secondary") t[i,2]<- length(res[[i]]@data$data[,1]) t[i,3]<- res[[i]]@data$args$log t[i,4:7]<- round(res[[i]]@data$summary[1:4],2) } t })##EndOf::renterTable() })##EndOf::shinyServer(function(input, output)RLumShiny/inst/shiny/KDE/www/0000755000176200001440000000000012743662035015512 5ustar liggesusersRLumShiny/inst/shiny/KDE/www/GitHub-Mark-32px.png0000644000176200001440000000326212743662035021067 0ustar liggesusersPNG  IHDR szztEXtSoftwareAdobe ImageReadyqe<$iTXtXML:com.adobe.xmp $IDATxėmhayL30A+R#f>IHکy(M)_o5 0+0Ėl&o{i^]u<{Yws}=uC>$L, }<w}8^ AO?p! xaяPKI3`'B>0QT1<+`}^nvkp^ƅF|1"Gp.*oO׀Vp ]߅jc8K$q 8jV`#`vmpGѢu!#}#:U_?_yhE $=;c*xNOo+&w)%K-R%6n'o">j/t³qoGW7j%2q GX?woibCÐAzbǰt \14|S.DZ]# b|H$(ʕohmqͱRP셣$,0Z20 tNvRW3K8Xk2 IO6F)X6of-/OK S, r RY~ApO|xˉN;@NZYJgnܟ) ߍz?\:qD/ Rz攟:})%8Cgo;ކ"Ғ͏JiYL!3czOϘiENr!/K(R "r옷lþ9nȉ'TxCP1N"9A]ՇW AANƗ}Ú.GJͥ:fx/kS//gtSusw)mo{[g|APS+z;~ѱߗ(ZU|%?{=vi! 5.^3 $v` uTAz(bs59$\{e3_dW_d S(9w{o[۶==v99!-@ x4X_?1_בr3B)@{r:M+ͤQTJEnXPckAEPS2NRJ5Q/ԶmYo/gT)(._qwi ǽѻadЋ\r !P-}1(*$yy !)R "a%_ +GPSh1!T/5ewR0[_=1_=N㼉!tpЛWZ+"S #w{_ ߼/nI6F9KڛhoחA0RD 5;Wo;qD;S?U)&$S-ȕ~eꎿ?9{N8#RzUYJ痟:obdr'*$_'<|9Gt $Wx^_PԆ5%e1=VNURLͯGK{ ^_<32!r YR }!}!"5Żmc?>㞿}R:WO9( i&}+I))=ϛuD/T _|5SQ@K!)EL 5l5sm ANRmAU/T j D!l \SR1[ .@P}L5АkAKǗUnX u?߻=_љ)+dBZYU2uԖ@~Q/eW_|=?~dݞ'Nhgd@}R*!,?u؛h Dɬ־usK;fx >zE=w2?)5HiFc`UP/T!AYxAEN]U)ݤ('TEP 洟?]?GN&[RB)fC?=FP 'D8KOӸm(R MA}OPBs#BAP;z!\h!,{*˱ci}?r qB(iRWv z dQ^ȜJ}BS@PB~^gu[;STJ+eR\GJ_qP#ˑSȳ{kHG>׎/+QqyN{%^[OzUP[*r bWӠ}R 7 o{w۶ǂ^DT5tWnS~갿 EHI)S=ϛuD%߲-j^)@KiHlkHBU%[W#-#)@k٧M)=okRZOP^-9ȷ]MDJGT)HT?" iB7;ez" "G֤U(-/_wǼ{eA}S OI D%ޒ[bj[BcVR3QSB]v%Ҷ<"YYIc7.텪TGPT } W#t˃E,[ʇ{JeAU/EƟ#}])EL&P/T ꭃLw*jUPS2)&F/56+#ٴo[l˹EP/T m~x% ^)@"?ncS\/2D%/GV_P#P;Y˛8ɥ/M\0}oKLmKZLz.ے7n[@ HJیS˛RX?c^he|\Ҏ^^oVS2h:#RZY0^(EAPWvTAˬ*r "d$AU5 u  ;H鱲nhNH+Ŗ\@@LYP HHґRh+*J,%A}Oz-PJkDNNǛHMYp,. 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The keyword \"Subtitle\" will only work if no plot subtitle is used.") ) ), selectInput(inputId = "summary.method", label = "Summary method", selected = "unweighted", choices = list("Unweighted" = "unweighted", "Weighted" = "weighted", "Monte Carlo" = "MCM")), tooltip(refId = "summary.method", attr = "for", text = "Keyword indicating the method used to calculate the statistic summary. See calc_Statistics for details."), checkboxGroupInput(inputId = "stats", label = "Parameters", selected = c("n","mean"), choices = c("n" = "n", "Mean" = "mean", "Median" = "median", "rel. Standard deviation" = "sd.rel", "abs. Standard deviation" = "sd.abs", "rel. Standard error" = "se.rel", "abs. Standard error" = "se.abs", "Skewness" = "skewness", "Kurtosis" = "kurtosis", "% in 2 sigma range" = "in.2s")), tooltip(refId = "stats", text = "Statistical parameters to be shown in the summary"), br(), div(align = "center", h5("Datapoint labels")), div(align = "center", checkboxGroupInput(inputId = "statlabels", inline = TRUE, label = NULL, choices = c("Min" = "min", "Max" = "max", "Median" = "median"))), tooltip(refId = "statlabels", text = "Additional labels of statistically important values in the plot."), br(), div(align = "center", h5("Error bars")), checkboxInput(inputId = "errorbars", label = "Show error bars", value = FALSE), tooltip(refId = "errorbars", text = "Option to show De-errors as error bars on De-points. Useful in combination with hidden y-axis and 2σ bar") ),##EndOf::Tab_2 # Tab 3: input that refer to the plot rather than the data tabPanel("Plot", div(align = "center", h5("Title")), fluidRow( column(width = 6, textInput(inputId = "main", label = "Title", value = "Abanico Plot") ), column(width = 6, textInput(inputId = "mtext", label = "Subtitle", value = "") ) ), div(align = "center", h5("Scaling")), # inject sliderInput from Server.R div(id="bwKDE", uiOutput(outputId = "bw") ), tooltip(refId = "bwKDE", text = "Bin width of the kernel density estimate"), fluidRow( column(width = 6, div(id="pratiodiv", sliderInput(inputId = "p.ratio", label = "Plot ratio", min=0.25, max=0.90, value=0.75, step=0.01, round= FALSE) ), tooltip(refId = "pratiodiv", text = "Relative space given to the radial versus the cartesian plot part, default is 0.75.") ), column(width = 6, sliderInput(inputId = "cex", label = "Scaling factor", min = 0.5, max = 2, value = 1.0, step = 0.1) ) ), br(), div(align = "center", h5("Centrality")), # centrality can either be a keyword or numerical input selectInput(inputId = "centrality", label = "Central Value", list("Mean" = "mean", "Median" = "median", "Weighted mean" = "mean.weighted", "Custom value" = "custom")), tooltip(refId = "centrality", text = "User-defined central value, used for centering of data."), conditionalPanel(condition = "input.centrality == 'custom'", uiOutput("centralityNumeric")), div(align = "center", h5("Dispersion")), selectInput(inputId = "dispersion", label = "Measure of dispersion", list("Quartile range" = "qr", "1 sigma" = "sd", "2 sigma" = "2sd", "Custom percentile range" = "custom")), tooltip(refId = "dispersion", text = "Measure of dispersion, used for drawing the polygon that depicts the spread in the dose distribution."), conditionalPanel(condition = "input.dispersion == 'custom'", numericInput(inputId = "cinn", label = "x % percentile", value = 25, min = 0, max = 100, step = 1)), div(align = "center", HTML("
2σ bar
")), fluidRow( column(width = 6, checkboxInput(inputId = "customSigBar", label = HTML("Customise 2σ bar"), value = FALSE) ), column(width = 6, checkboxInput(inputId = "addBar", label = HTML("Second 2σ bar"), value = FALSE) ) ), fluidRow( column(width = 6, conditionalPanel(condition = "input.customSigBar == true", numericInput(inputId = "sigmabar1", label = HTML("2σ bar 1"), min = 0, max = 100, value = 60) ) ), column(width = 6, conditionalPanel(condition = "input.customSigBar == true", numericInput(inputId = "sigmabar2", label = HTML("2σ bar 2"), min = 0, max = 100, value = 100) ) ) ), div(align = "center", h5("Central line")), fluidRow( column(width = 6, numericInput(inputId = "lwd", label = "Line width #1", min = 0, max = 5, value = 1) ), column(width = 6, numericInput(inputId = "lwd2", label = "Line width #2", min = 0, max = 5, value = 1) ) ), fluidRow( column(width = 6, selectInput(inputId = "lty", label = "Line type", selected = 2, choices = list("Blank" = 0, "Solid" = 1, "Dashed" = 2, "Dotted" = 3, "Dot dash" = 4, "Long dash" = 5, "Two dash" = 6)) ), column(width = 6, selectInput(inputId = "lty2", label = "Line type", selected = 2, choices = list("Blank" = 0, "Solid" = 1, "Dashed" = 2, "Dotted" = 3, "Dot dash" = 4, "Long dash" = 5, "Two dash" = 6)) ) ), div(align = "center", h5("Further options")), fluidRow( column(width = 6, checkboxInput(inputId = "rug", label = "Add rug", value = FALSE), tooltip(refId = "rug", text = "Option to add a rug to the KDE part, to indicate the location of individual values") ), column(width = 6, checkboxInput(inputId = "rotate", label = "Rotate plot", value = FALSE), tooltip(refId = "rotate", text = "Option to rotate the plot by 90°.") ) ), checkboxInput(inputId = "boxplot", label = "Boxplot", value = FALSE), tooltip(refId = "boxplot", text = "Option to add a boxplot to the dispersion part."), checkboxInput(inputId = "kde", label = "KDE", value = TRUE), tooltip(refId = "kde", text = "Option to add a KDE plot to the dispersion part."), checkboxInput(inputId = "histogram", label = "Histogram", value = TRUE), tooltip(refId = "histogram", text = "Option to add a histogram to the dispersion part. Only meaningful when not more than one data set is plotted."), checkboxInput(inputId = "dots", label = "Dots", value = TRUE), tooltip(refId = "dots", text = "Option to add a dot plot to the dispersion part. If number of dots exceeds space in the dispersion part, a square indicates this.") ),##EndOf::Tab_3 # Tab 4: modify axis parameters tabPanel("Axis", div(align = "center", h5("X-axis")), fluidRow( column(width = 6, textInput(inputId = "xlab1", label = "Label x-axis (upper)", value = "Relative error [%]") ), column(width = 6, textInput(inputId = "xlab2", label = "Label x-axis (lower)", value = "Precision") ) ), # inject sliderInput from Server.R uiOutput(outputId = "xlim"), br(), div(align = "center", h5("Y-axis")), checkboxInput(inputId = "yaxis", label = "Show y-axis", value = TRUE), tooltip(refId = "yaxis", text = "Option to hide y-axis labels. Useful for data with small scatter."), textInput(inputId = "ylab", label = "Label y-axis", value = "Standardised estimate"), uiOutput("ylim"), br(), div(align = "center", h5("Z-axis")), checkboxInput(inputId = "logz", label = "Logarithmic z-axis", value = TRUE), tooltip(refId = "logz", text = "Option to display the z-axis in logarithmic scale."), textInput(inputId = "zlab", label = "Label z-axis", value = "Equivalent dose [Gy]"), # inject sliderInput from Server.R uiOutput(outputId = "zlim") ),##EndOf::Tab_4 # Tab 5: modify data point representation tabPanel("Datapoints", div(align = "center", h5("Primary data set")), fluidRow( column(width = 6, selectInput(inputId = "pch", label = "Style", selected = "17", choices = c("Square"= "1", "Circle"="2", "Triangle point up"="3", "Plus"="4", "Cross"="5", "Diamond"="6", "Triangle point down"="7", "Square cross"="8", "Star"="9", "Diamond plus"="10", "Circle plus"="11", "Triangles up and down"="12", "Square plus"="13", "Circle cross"="14", "Square and Triangle down"="15", "filled Square"="16", "filled Circle"="17", "filled Triangle point up"="18", "filled Diamond"="19", "solid Circle"="20", "Bullet (smaller Circle)"="21", "Custom"="custom")) ), column(width = 6, # show only if custom symbol is desired conditionalPanel(condition = "input.pch == 'custom'", textInput(inputId = "custompch", label = "Insert character", value = "?")) ) ), fluidRow( column(width = 6, selectInput(inputId = "color", label = "Datapoint color", choices = list("Black" = "black", "Grey" = "grey50", "Red" = "#b22222", "Green" = "#6E8B3D", "Blue" = "#428bca", "Custom" = "custom")) ), column(width = 6, # show only if custom color is desired conditionalPanel(condition = "input.color == 'custom'", HTML("Choose a color
"), jscolorInput(inputId = "jscol1")) ) ), br(), div(align = "center", h5("Secondary data set")), fluidRow( column(width = 6, ## DATA SET 2 selectInput(inputId = "pch2", label = "Style", selected = "17", choices = c("Square"= "1", "Circle"="2", "Triangle point up"="3", "Plus"="4", "Cross"="5", "Diamond"="6", "Triangle point down"="7", "Square cross"="8", "Star"="9", "Diamond plus"="10", "Circle plus"="11", "Triangles up and down"="12", "Square plus"="13", "Circle cross"="14", "Square and Triangle down"="15", "filled Square"="16", "filled Circle"="17", "filled Triangle point up"="18", "filled Diamond"="19", "solid Circle"="20", "Bullet (smaller Circle)"="21", "Custom"="custom")) ), column(width = 6, # show only if custom symbol is desired conditionalPanel(condition = "input.pch2 == 'custom'", textInput(inputId = "custompch2", label = "Insert character", value = "?")) ) ), fluidRow( column(width = 6, selectInput(inputId = "color2", label = "Datapoint color", selected = "#b22222", choices = list("Black" = "black", "Grey" = "grey50", "Red" = "#b22222", "Green" = "#6E8B3D", "Blue" = "#428bca", "Custom" = "custom")) ), column(width = 6, # show only if custom color is desired conditionalPanel(condition = "input.color2 == 'custom'", HTML("Choose a color
"), jscolorInput(inputId = "jscol2")) ) ) ),##EndOf::Tab_5 # Tab 6: add additional lines to the plot tabPanel("Lines", helpText("Here you can add additional lines."), # options for custom lines: # 1 - z-value, 2 - color, 3 - label, 4 - line type # only the options for the first line are shown fluidRow( column(width = 6, numericInput(inputId = "line1", label = strong("Line #1"), value = NA, min = 0) ), tooltip(refId = "line1", text = "Numeric values of the additional lines to be added."), column(width = 6, selectInput(inputId = "linelty1", label = "Line type", selected = 1, choices = list("Blank" = 0, "Solid" = 1, "Dashed" = 2, "Dotted" = 3, "Dot dash" = 4, "Long dash" = 5, "Two dash" = 6)) ) ), fluidRow( column(width = 6, HTML("Choose a color
"), jscolorInput(inputId = "colline1") ), column(width = 6, textInput(inputId = "labline1", label = "Label", value = "") ) ), # conditional chain: if valid input (i.e. the z-value is > 0) is provided # for the previous line, show options for a new line (currently up to eight) conditionalPanel(condition = "input.line1 > 0", fluidRow( column(width = 6, numericInput(inputId = "line2", strong("Line #2"), NA, min = 0)), column(width = 6, selectInput(inputId = "linelty2", label = "Line type",selected = 1, choices = list("Blank" = 0, "Solid" = 1, "Dashed" = 2, "Dotted" = 3, "Dot dash" = 4, "Long dash" = 5, "Two dash" = 6))) ), fluidRow( column(width = 6, HTML("Choose a color
"),jscolorInput(inputId = "colline2")), column(width = 6, textInput("labline2","Label",value = "")) ) ), conditionalPanel(condition = "input.line2 > 0", fluidRow( column(width = 6, numericInput(inputId = "line3", strong("Line #3"), NA, min = 0)), column(width = 6, selectInput(inputId = "linelty3", label = "Line type",selected = 1, choices = list("Blank" = 0, "Solid" = 1, "Dashed" = 2, "Dotted" = 3, "Dot dash" = 4, "Long dash" = 5, "Two dash" = 6))) ), fluidRow( column(width = 6, HTML("Choose a color
"),jscolorInput(inputId = "colline3")), column(width = 6, textInput("labline3","Label",value = "")) ) ), conditionalPanel(condition = "input.line3 > 0", fluidRow( column(width = 6, numericInput(inputId = "line4", strong("Line #4"), NA, min = 0)), column(width = 6, selectInput(inputId = "linelty4", label = "Line type",selected = 1, choices = list("Blank" = 0, "Solid" = 1, "Dashed" = 2, "Dotted" = 3, "Dot dash" = 4, "Long dash" = 5, "Two dash" = 6))) ), fluidRow( column(width = 6, HTML("Choose a color
"),jscolorInput(inputId = "colline4")), column(width = 6, textInput("labline4","Label",value = "")) ) ), conditionalPanel(condition = "input.line4 > 0", fluidRow( column(width = 6, numericInput(inputId = "line5", strong("Line #5"), NA, min = 0)), column(width = 6, selectInput(inputId = "linelty5", label = "Line type",selected = 1, choices = list("Blank" = 0, "Solid" = 1, "Dashed" = 2, "Dotted" = 3, "Dot dash" = 4, "Long dash" = 5, "Two dash" = 6))) ), fluidRow( column(width = 6, HTML("Choose a color
"),jscolorInput(inputId = "colline5")), column(width = 6, textInput("labline5","Label",value = "")) ) ), conditionalPanel(condition = "input.line5 > 0", fluidRow( column(width = 6, numericInput(inputId = "line6", strong("Line #6"), NA, min = 0)), column(width = 6, selectInput(inputId = "linelty6", label = "Line type",selected = 1, choices = list("Blank" = 0, "Solid" = 1, "Dashed" = 2, "Dotted" = 3, "Dot dash" = 4, "Long dash" = 5, "Two dash" = 6))) ), fluidRow( column(width = 6, HTML("Choose a color
"),jscolorInput(inputId = "colline6")), column(width = 6, textInput("labline6","Label",value = "")) ) ), conditionalPanel(condition = "input.line6 > 0", fluidRow( column(width = 6, numericInput(inputId = "line7", strong("Line #7"), NA, min = 0)), column(width = 6, selectInput(inputId = "linelty7", label = "Line type",selected = 1, choices = list("Blank" = 0, "Solid" = 1, "Dashed" = 2, "Dotted" = 3, "Dot dash" = 4, "Long dash" = 5, "Two dash" = 6))) ), fluidRow( column(width = 6, HTML("Choose a color
"),jscolorInput(inputId = "colline7")), column(width = 6, textInput("labline7","Label",value = "")) ) ), conditionalPanel(condition = "input.line7 > 0", fluidRow( column(width = 6, numericInput(inputId = "line8", strong("Line #8"), NA, min = 0)), column(width = 6, selectInput(inputId = "linelty8", label = "Line type",selected = 1, choices = list("Blank" = 0, "Solid" = 1, "Dashed" = 2, "Dotted" = 3, "Dot dash" = 4, "Long dash" = 5, "Two dash" = 6))) ), fluidRow( column(width = 6, HTML("Choose a color
"),jscolorInput(inputId = "colline8")), column(width = 6, textInput("labline8","Label",value = "")) ) ) ),##EndOf::Tab_6 # Tab 7: modify the 2-sigma bar (radial plot), grid (both) and polygon (KDE) tabPanel("Bars & Grid", div(align = "center", h5("Dispersion bar")), fluidRow( column(width = 6, selectInput(inputId = "polygon", label = "Dispersion bar color #1", choices = list("Grey" = "grey80", "Custom" = "custom", "None" = "none")), tooltip(refId = "polygon", attr = "for", text = "Colour of the polygon showing the dose dispersion around the central value.") ), column(width = 6, selectInput(inputId = "polygon2", label = "Dispersion bar color #2", choices = list("Grey" = "grey80", "Custom" = "custom", "None" = "none")) ) ), fluidRow( column(width = 6, # show only if custom color is desired conditionalPanel(condition = "input.polygon == 'custom'", jscolorInput(inputId = "rgbPolygon", label = "Choose a color")) ), column(width = 6, # show only if custom color is desired conditionalPanel(condition = "input.polygon2 == 'custom'", jscolorInput(inputId = "rgbPolygon2", label = "Choose a color")) ) ), sliderInput(inputId = "alpha.polygon", label = "Transparency", min = 0, max = 100, step = 1, value = 66), br(), div(align = "center", HTML("
2σ bar
")), fluidRow( column(width = 6, selectInput(inputId = "bar", label = HTML("2σ bar color"), choices = list("Grey" = "grey50", "Custom" = "custom", "None" = "none")), tooltip(refId = "bar", attr = "for", text = "Colour of the bar showing the 2-sigma range of the dose error around the central value.") ), column(width = 6, selectInput(inputId = "bar2", label = HTML("2σ bar color #2"), choices = list("Grey" = "grey50", "Custom" = "custom", "None" = "none")) ) ), fluidRow( column(width = 6, # show only if custom color is desired conditionalPanel(condition = "input.bar == 'custom'", jscolorInput(inputId = "rgbBar", label = "Choose a color")) ), column(width = 6, # show only if custom color is desired conditionalPanel(condition = "input.bar2 == 'custom'", jscolorInput(inputId = "rgbBar2", label = "Choose a color")) ) ), sliderInput(inputId = "alpha.bar", label = "Transparency", min = 0, max = 100, step = 1, value = 66), br(), div(align = "center", h5("Grid")), fluidRow( column(width = 6, selectInput(inputId = "grid", label = "Grid color", selected = "none", list("Grey" = "grey90", "Custom" = "custom", "None" = "none")) ), column(width = 6, # show only if custom color is desired conditionalPanel(condition = "input.grid == 'custom'", jscolorInput(inputId = "rgbGrid", label = "Choose a color")) ) ), sliderInput(inputId = "alpha.grid", label = "Transparency", min = 0, max = 100, step = 1, value = 50), br(), div(align = "center", h5("Frame")), selectInput(inputId = "frame", label = "Frame", selected = 1, choices = list("No frame" = 0, "Origin at {0,0}" = 1, "Anchors at {0,-2}, {0,2}" = 2, "Rectangle" = 3)) ),##EndOf::Tab_7 # Tab 8: add and customize legend tabPanel("Legend", div(align = "center", h5("Legend")), fluidRow( column(width = 6, checkboxInput(inputId = "showlegend", label = "Show legend", value = FALSE), tooltip(refId = "showlegend", text = "Legend content to be added to the plot.") ), column(width = 6, selectInput(inputId = "legend.pos", label = "Legend position", selected = "bottomleft", choices = c("Top" = "top", "Top left" = "topleft", "Top right"= "topright", "Center" = "center", "Bottom" = "bottom", "Bottom left" = "bottomleft", "Bottom right" = "bottomright")) ) ), fluidRow( column(width = 6, textInput(inputId = "legendname", label = "Primary data label", value = "primary data") ), column(width = 6, textInput(inputId = "legendname2", label = "Secondary data label", value = "secondary data") ) ) ),##EndOf::Tab_8 # Tab 9: Filter data tabPanel("Filter", div(align = "center", h5("Primary data set")), selectInput(inputId = "filter.prim", label = "Choose values to exclude", choices = "", multiple = TRUE, selected = ""), div(align = "center", h5("Secondary data set")), selectInput(inputId = "filter.sec", label = "Choose values to exclude", choices = "", multiple = TRUE, selected = ""), actionButton(inputId = "exclude", label = "Exclude") ),##EndOf::Tab_9 # Tab 10: Layout tabPanel("Layout", div(align = "center", h5("Layout")), div(id = "layout", selectInput(inputId = "layout", label = "Choose layout", selected = "default", choices = c("Default"="default", "Journal"="journal")) ), tooltip(refId = "layout", placement = "top", text = "The optional parameter layout allows to modify the entire plot more sophisticated. Each element of the plot can be addressed and its properties can be defined. This includes font type, size and decoration, colours and sizes of all plot items. To infer the definition of a specific layout style cf. get_Layout() or type eg. for the layout type \"journal\" get_Layout(\"journal\"). A layout type can be modified by the user by assigning new values to the list object.") ), # Tab 10: save plot as pdf, wmf or eps tabPanel("Export", radioButtons(inputId = "fileformat", label = "Fileformat", selected = "pdf", choices = c("PDF (Portable Document Format)" = "pdf", "SVG (Scalable Vector Graphics)" = "svg", "EPS (Encapsulated Postscript)" = "eps")), textInput(inputId = "filename", label = "Filename", value = "Abanico Plot"), fluidRow( column(width = 6, numericInput(inputId = "imgheight", label = "Image height", value = 7) ), column(width = 6, numericInput(inputId = "imgwidth", label = "Image width", value = 7) ) ), selectInput(inputId = "fontfamily", label = "Font", selected = "Helvetica", choices = c("Helvetica" = "Helvetica", "Helvetica Narrow" = "Helvetica Narrow", "Times" = "Times", "Courier" = "Courier", "Bookman" = "Bookman", "Palatino" = "Palatino")), tags$hr(), downloadButton(outputId = "exportFile", label = "Download plot"), tags$hr(), helpText("Additionally, you can download a corresponding .R file that contains", "a fully functional script to reproduce the plot in your R environment!"), downloadButton(outputId = "exportScript", label = "Download R script") ),##EndOf::Tab_8 # Tab 10: further information tabPanel("About", hr(), div(align = "center", # HTML code to include a .png file in the tab; the image file must be in # a subfolder called "wwww" img(src="RL_Logo.png", height = 100, width = 100, alt = "R.Lum"), p("Links:"), a(href = "http://www.r-luminescence.de", "R.Luminescence project page", target="_blank"), br(), a(href = "https://forum.r-luminescence.de", "Message board", target="_blank"), br(), a(href = "http://zerk.canopus.uberspace.de/R.Lum", "Online application", target="_blank"), br(),hr(), img(src='GitHub-Mark-32px.png', width='32px', height='32px'), br(), a(href = "https://github.com/tzerk/RLumShiny/tree/master/inst/shiny/abanico", "See the code at GitHub!", target="_blank") )#/div )##EndOf::Tab_9 )##EndOf::tabsetPanel ),##EndOf::sidebarPanel # 3 - output panel mainPanel(width = 7, # insert css code inside of the generated HTML file: # allow open dropdown menus to reach over the container tags$head(tags$style(type="text/css",".tab-content {overflow: visible;}")), tags$head(includeCSS("www/style.css")), # divide output in separate tabs via tabsetPanel tabsetPanel( tabPanel("Plot", plotOutput(outputId = "main_plot", height = "500px")), tabPanel("Primary data set", fluidRow(column(width = 12, dataTableOutput("dataset")))), tabPanel("Secondary data set", dataTableOutput("dataset2")), tabPanel("Central Age Model", dataTableOutput("CAM")), tabPanel("R plot code", verbatimTextOutput("plotCode")) )###EndOf::tabsetPanel )##EndOf::mainPanel )##EndOf::shinyUI(pageWithSidebar)RLumShiny/inst/shiny/abanico/server.R0000644000176200001440000004636312743662035017324 0ustar liggesusers## Server.R library(Luminescence) library(RLumShiny) library(shiny) # load example data data(ExampleData.DeValues, envir = environment()) data <- ExampleData.DeValues$CA1 ## MAIN FUNCTION shinyServer(function(input, output, session) { ### GET DATA SETS Data<- reactive({ ### GET DATA if(!is.null(datGet())) { if(!is.null(datGet2())) { data<- list(datGet(), datGet2()) } else { data<- list(datGet()) } } else { data<- list(data) } ### DATA FILTER input$exclude sub<- data isolate({ filter.prim<- input$filter.prim filter.sec<- input$filter.sec }) if(!is.null(filter.prim)) { index<- grep(paste(filter.prim, collapse = "|"), data[[1]][,1]) sub[[1]]<- data[[1]][-index,] } if(length(data) == 2 && !is.null(filter.sec)) { index<- grep(paste(filter.sec, collapse = "|"), data[[2]][,1]) sub[[2]]<- data[[2]][-index,] } stillSelected.prim<- filter.prim stillSelected.sec<- filter.sec updateSelectInput(session, inputId = "filter.prim", choices = sort(data[[1]][,1]), selected = stillSelected.prim) if(length(data) == 2) { updateSelectInput(session, inputId = "filter.sec", choices = sort(data[[2]][,1]), selected = stillSelected.sec) } data<- sub return(data) }) # check and read in file (DATA SET 1) datGet<- reactive({ inFile<- input$file1 if(is.null(inFile)) return(NULL) # if no file was uploaded return NULL return(read.table(file = inFile$datapath, # inFile[1] contains filepath sep = input$sep, quote = "", header = input$headers)) # else return file }) # check and read in file (DATA SET 2) datGet2<- reactive({ inFile2<- input$file2 if(is.null(inFile2)) return(NULL) # if no file was uploaded return NULL return(read.table(file = inFile2$datapath, # inFile[1] contains filepath sep = input$sep, quote = "", header = input$headers)) # else return file }) # dynamically inject sliderInput for x-axis range output$xlim<- renderUI({ data<- Data() if(input$logz == TRUE) { sd<- unlist(lapply(data, function(x) x[,2]/x[,1])) } else { sd<- unlist(lapply(data, function(x) x[,2])) } prec<- 1/sd sliderInput(inputId = "xlim", sep="", label = "Range x-axis", min = 0, max = round(max(prec)*2, 3), value = c(0, max(prec)*1.05)) })## EndOf::renderUI() # dynamically inject sliderInput for z-axis range output$zlim<- renderUI({ data<- unlist(lapply(Data(), function(x) x[,1])) min<- min(data) max<- max(data) sliderInput(inputId = "zlim", sep="", label = "Range z-axis", min = min*0.25, max = round(max*1.75, 3), value = c(min*0.8, max*1.2)) })## EndOf::renderUI() output$ylim<- renderUI({ ylim<- plot_AbanicoPlot(Data(), output = TRUE)$ylim sliderInput(inputId = "ylim", sep="", label = "Range y-axis", min = ylim[1]*4, max = round(ylim[2]*4, 3), value = c(ylim[1], ylim[2])) }) # dynamically inject sliderInput for KDE bandwidth output$bw<- renderUI({ data<- unlist(lapply(Data(), function(x) x[,1])) if(input$logz == TRUE) { data<- log(data) min<- 0.001 value<- bw.nrd0(data)*2 max<- value*2 } else { value<- bw.nrd0(data) min<- value/4 max<- value*4 } sliderInput(inputId = "bw", sep="", label = "KDE bandwidth", min = round(min, 3), max = round(max, 3), value = value) })## EndOf::renderUI() # observe({ # # case: 1 data set, 2 sigma bars --> switch to custom value # if(input$addBar == TRUE && is.null(datGet2())) { # updateSelectInput(session = session, inputId = "centrality", # label = "Centrality", # selected = "custom") # } # # case: 1 data set, 1 sigma bars --> return to mean centrality # if(input$addBar == FALSE && is.null(datGet2())) { # updateSelectInput(session = session, inputId = "centrality", # label = "Centrality", # selected = "mean") # } # }) output$centralityNumeric<- renderUI({ #update_centrality() if(!is.null(datGet())){ data<- datGet() } numericInput(inputId = "centralityNumeric", label = "Value", value = round(mean(data[,1]), 2), step = 0.01) }) # render Abanico Plot output$main_plot <- renderPlot({ # refresh plot on button press input$refresh # progress bar progress<- Progress$new(session, min = 0, max = 5) progress$set(message = "Calculation in progress", detail = "Retrieve data") on.exit(progress$close()) # make sure that input panels are registered on non-active tabs. # by default tabs are suspended and input variables are hence # not available outputOptions(x = output, name = "bw", suspendWhenHidden = FALSE) outputOptions(x = output, name = "zlim", suspendWhenHidden = FALSE) outputOptions(x = output, name = "xlim", suspendWhenHidden = FALSE) outputOptions(x = output, name = "ylim", suspendWhenHidden = FALSE) outputOptions(x = output, name = "centralityNumeric", suspendWhenHidden = FALSE) # get data data<- Data() # update progress bar progress$set(value = 1) progress$set(message = "Calculation in progress", detail = "Get values") # check if any summary stats are activated, else NA ifelse(input$summary, summary<- input$stats, summary<- NA) # if custom datapoint color get RGB code from separate input panel if(input$color == "custom") { color<- ifelse(input$jscol1 == "", "black", input$jscol1) } else { color<- input$color } if(!is.null(datGet2())) { # if custom datapoint color get RGB code from separate input panel if(input$color2 == "custom") { if(input$jscol2 == "") { color2<- "black" } else { color2<- input$jscol2 } } else { color2<- input$color2 } } else { color2<- "black" #adjustcolor("white", alpha.f = 0) } # if custom datapoint style get char from separate input panel pch<- ifelse(input$pch == "custom", input$custompch, as.integer(input$pch)-1) # if custom datapoint style get char from separate input panel pch2<- ifelse(input$pch2 == "custom", input$custompch2, as.integer(input$pch2)-1) # update progress bar progress$set(value = 2) progress$set(message = "Calculation in progress", detail = "Combine values") # create numeric vector of lines line<- as.numeric(c(input$line1, input$line2, input$line3, input$line4, input$line5, input$line6, input$line7, input$line8)) # create char vector of line colors line.col<- c(input$colline1, input$colline2, input$colline3, input$colline4, input$colline5, input$colline6, input$colline7, input$colline8) line.col[which(line.col=="#")] <- "#FFFFFF" # create char vector of line labels line.label<- c(input$labline1, input$labline2, input$labline3, input$labline4, input$labline5, input$labline6, input$labline7, input$labline8) # create integer vector of line types line.lty<- as.integer(c(input$linelty1, input$linelty2, input$linelty3, input$linelty4, input$linelty5, input$linelty6, input$linelty7, input$linelty8)) # update progress bar progress$set(value = 3) progress$set(message = "Calculation in progress", detail = "Get values") # if custom polygon color get RGB from separate input panel or "none" if(input$polygon == "custom") { polygon.col<- adjustcolor(col = input$rgbPolygon, alpha.f = input$alpha.polygon/100) } else { polygon.col<- ifelse(input$polygon == "none", input$polygon, adjustcolor(col = input$polygon, alpha.f = input$alpha.polygon/100)) } # if custom polygon color get RGB from separate input panel or "none" # (secondary data set) if(input$polygon2 == "custom") { polygon.col2<- adjustcolor(col = input$rgbPolygon2, alpha.f = input$alpha.polygon/100) } else { polygon.col2<- ifelse(input$polygon2 == "none", input$polygon2, adjustcolor(col = input$polygon2, alpha.f = input$alpha.polygon/100)) } # if custom bar color get RGB from separate input panel or "none" if(input$bar == "custom") { bar.col<- adjustcolor(col = input$rgbBar, alpha.f = input$alpha.bar/100) } else { bar.col<- ifelse(input$bar == "none", input$bar, adjustcolor(col = input$bar, alpha.f = input$alpha.bar/100)) } # if custom bar color get RGB from separate input panel or "none" # SECONDARY DATA SET if(input$bar2 == "custom") { bar.col2<- adjustcolor(col = input$rgbBar2, alpha.f = input$alpha.bar/100) } else { bar.col2<- ifelse(input$bar2 == "none", input$bar, adjustcolor(col = input$bar2, alpha.f = input$alpha.bar/100)) } # if custom grid color get RGB from separate input panel or "none" if(input$grid == "custom") { grid.col<- adjustcolor(col = input$rgbGrid, alpha.f = input$alpha.grid/100) } else { grid.col<- ifelse(input$grid == "none", input$grid, adjustcolor(col = input$grid, alpha.f = input$alpha.grid/100)) } # update progress bar progress$set(value = 4) progress$set(message = "Calculation in progress", detail = "Almost there...") # workaround: if no legend wanted set label to NA and hide # symbol on coordinates -999, -999 if(input$showlegend == FALSE) { legend<- c(NA,NA) legend.pos<- c(-999,-999) } else { if(!is.null(datGet2())) { legend<- c(input$legendname, input$legendname2) legend.pos<- input$legend.pos } else { legend<- c(input$legendname, "") legend.pos<- input$legend.pos } } # TODO: arg 'bar' handling (custom values, 1 or 2 bars) if (input$customSigBar) { if (!input$addBar) bar <- input$sigmabar1 if (input$addBar) bar <- c(input$sigmabar1, input$sigmabar2) } else { bar <- TRUE } # check wether a keyword or a numeric value is used for # centrality if(input$centrality == "custom") { centrality<- input$centralityNumeric } else { centrality<- input$centrality } # check wether predefined or custom dispersion dispersion<- ifelse(input$dispersion == "custom", paste("p", input$cinn, sep=""), input$dispersion) # validate(need()) makes sure that all data are available to # renderUI({}) before plotting and will wait until there validate(need(expr = input$bw, message = ''), need(expr = input$zlim, message = ''), need(expr = input$ylim, message = ''), need(expr = input$centralityNumeric, message = 'Waiting for data... Please wait!')) # save all arguments in a list args<- list(data = data, y.axis = input$yaxis, bw = input$bw, bar = bar, dispersion = dispersion, plot.ratio = input$p.ratio, z.0 = centrality, log.z = input$logz, summary = summary, summary.pos = input$sumpos, summary.method = input$summary.method, col = c(color,color2), pch = c(pch,pch2), zlab = input$zlab, main = input$main, zlim = input$zlim, cex = input$cex, mtext = input$mtext, stats = input$statlabels, error.bars = input$errorbars, line = line, line.col = line.col, line.label = line.label, line.lty = line.lty, polygon.col = c(polygon.col,polygon.col2), bar.col = c(bar.col, bar.col2), grid.col = grid.col, legend = legend, legend.pos = legend.pos, na.rm = input$naExclude, lwd = c(input$lwd, input$lwd2), xlab = c(input$xlab1, input$xlab2), ylab = input$ylab, lty = c(as.integer(input$lty), as.integer(input$lty2)), xlim = input$xlim, ylim = input$ylim, rug = input$rug, layout = input$layout, rotate = input$rotate, boxplot = input$boxplot, kde = input$kde, hist = input$histogram, dots = input$dots, frame = input$frame) progress$set(value = 5) progress$set(message = "Calculation in progress", detail = "Ready to plot") # plot Abanico Plot do.call(what = plot_AbanicoPlot, args = args) # prepare code as text output if (is.null(input$sep)) updateRadioButtons(session, "fileformat", selected = "\t") if(input$sep == "\t") verb.sep<- "\\t" else verb.sep<- input$sep str1 <- paste("data <- read.delim(file, header = ",input$headers, ", sep= '", verb.sep,"')", sep = "") if(!is.null(datGet2())) { str2 <- "file2<- file.choose()" str3 <- paste("data2 <- read.delim(file2, header = ",input$headers, ", sep= '", verb.sep,"')", sep= "") str4 <- "data<- list(data, data2)" str1 <- paste(str1, str2, str3, str4, sep = "\n") } header <- paste("# To reproduce the plot in your local R environment", "# copy and run the following code to your R console.", "library(Luminescence)", "file<- file.choose()", str1, "\n", sep = "\n") names <- names(args) verb.arg <- paste(mapply(function(name, arg) { if (all(inherits(arg, "character"))) arg <- paste0("'", arg, "'") if (length(arg) > 1) arg <- paste0("c(", paste(arg, collapse = ", "), ")") if (is.null(arg)) arg <- "NULL" paste(name, "=", arg) }, names[-1], args[-1]), collapse = ",\n") funCall <- paste0("plot_AbanicoPlot(data = data,\n", verb.arg, ")") code.output <- paste0(header, funCall, collapse = "\n") # nested renderText({}) for code output on "R plot code" tab output$plotCode<- renderText({ code.output })##EndOf::renderText({}) output$exportScript <- downloadHandler( filename = function() { paste(input$filename, ".", "R", sep="") }, content = function(file) { write(code.output, file) },#EO content =, contentType = "text" )#EndOf::dowmloadHandler() # nested downloadHandler() to print plot to file output$exportFile <- downloadHandler( filename = function() { paste(input$filename, ".", input$fileformat, sep="") }, content = function(file) { # determine desired fileformat and set arguments if(input$fileformat == "pdf") { pdf(file, width = input$imgwidth, height = input$imgheight, paper = "special", useDingbats = FALSE, family = input$fontfamily) } if(input$fileformat == "svg") { svg(file, width = input$imgwidth, height = input$imgheight, family = input$fontfamily) } if(input$fileformat == "eps") { postscript(file, width = input$imgwidth, height = input$imgheight, paper = "special", family = input$fontfamily) } # plot Abanico Plot do.call(what = plot_AbanicoPlot, args = args) dev.off() },#EO content =, contentType = "image" )#EndOf::dowmloadHandler() })##EndOf::renderPlot({}) Selected<- reactive({ input$refresh }) # renderTable() that prints the data to the second tab output$dataset<- renderDataTable( options = list(pageLength = 10, autoWidth = FALSE), callback = "function(table) { table.on('click.dt', 'tr', function() { $(this).toggleClass('selected'); Shiny.onInputChange('rows', table.rows('.selected').data().toArray()); }); }", { if(!is.null(datGet())) { data<- datGet() colnames(data)<- c("De","De error") data } else { colnames(data)<- c("De","De error") Selected() data } })##EndOf::renterTable() # renderTable() that prints the secondary data to the second tab output$dataset2<- renderDataTable( options = list(pageLength = 10, autoWidth = FALSE), callback = "function(table) { table.on('click.dt', 'tr', function() { $(this).toggleClass('selected'); Shiny.onInputChange('rows', table.rows('.selected').data().toArray()); }); }", { if(!is.null(datGet2())) { data<- datGet2() colnames(data)<- c("De","De error") data } else { } })##EndOf::renterTable() # renderTable() to print the results of the # central age model (CAM) output$CAM<- renderDataTable( options = list(pageLength = 10, autoWidth = FALSE), { data<- Data() t<- as.data.frame(matrix(nrow = length(data), ncol = 7)) colnames(t)<- c("Data set","n", "log data", "Central dose", "SE abs.", "OD (%)", "OD error (%)") res<- lapply(data, function(x) { calc_CentralDose(x, verbose = FALSE, plot = FALSE) }) for(i in 1:length(res)) { t[i,1]<- ifelse(i==1,"pimary","secondary") t[i,2]<- length(res[[i]]@data$data[,1]) t[i,3]<- res[[i]]@data$args$log t[i,4:7]<- round(res[[i]]@data$summary[1:4],2) } t })##EndOf::renterTable() })##EndOf::shinyServer(function(input, output)RLumShiny/inst/shiny/abanico/www/0000755000176200001440000000000012743662035016503 5ustar liggesusersRLumShiny/inst/shiny/abanico/www/GitHub-Mark-32px.png0000644000176200001440000000326212743662035022060 0ustar liggesusersPNG  IHDR szztEXtSoftwareAdobe ImageReadyqe<$iTXtXML:com.adobe.xmp $IDATxėmhayL30A+R#f>IHکy(M)_o5 0+0Ėl&o{i^]u<{Yws}=uC>$L, }<w}8^ AO?p! xaяPKI3`'B>0QT1<+`}^nvkp^ƅF|1"Gp.*oO׀Vp ]߅jc8K$q 8jV`#`vmpGѢu!#}#:U_?_yhE $=;c*xNOo+&w)%K-R%6n'o">j/t³qoGW7j%2q GX?woibCÐAzbǰt \14|S.DZ]# b|H$(ʕohmqͱRP셣$,0Z20 tNvRW3K8Xk2 IO6F)X6of-/OK S, r RY~ApO|xˉN;@NZYJgnܟ) ߍz?\:qD/ Rz攟:})%8Cgo;ކ"Ғ͏JiYL!3czOϘiENr!/K(R "r옷lþ9nȉ'TxCP1N"9A]ՇW AANƗ}Ú.GJͥ:fx/kS//gtSusw)mo{[g|APS+z;~ѱߗ(ZU|%?{=vi! 5.^3 $v` uTAz(bs59$\{e3_dW_d S(9w{o[۶==v99!-@ x4X_?1_בr3B)@{r:M+ͤQTJEnXPckAEPS2NRJ5Q/ԶmYo/gT)(._qwi ǽѻadЋ\r !P-}1(*$yy !)R "a%_ +GPSh1!T/5ewR0[_=1_=N㼉!tpЛWZ+"S #w{_ ߼/nI6F9KڛhoחA0RD 5;Wo;qD;S?U)&$S-ȕ~eꎿ?9{N8#RzUYJ痟:obdr'*$_'<|9Gt $Wx^_PԆ5%e1=VNURLͯGK{ ^_<32!r YR }!}!"5Żmc?>㞿}R:WO9( i&}+I))=ϛuD/T _|5SQ@K!)EL 5l5sm ANRmAU/T j D!l \SR1[ .@P}L5АkAKǗUnX u?߻=_љ)+dBZYU2uԖ@~Q/eW_|=?~dݞ'Nhgd@}R*!,?u؛h Dɬ־usK;fx >zE=w2?)5HiFc`UP/T!AYxAEN]U)ݤ('TEP 洟?]?GN&[RB)fC?=FP 'D8KOӸm(R MA}OPBs#BAP;z!\h!,{*˱ci}?r qB(iRWv z dQ^ȜJ}BS@PB~^gu[;STJ+eR\GJ_qP#ˑSȳ{kHG>׎/+QqyN{%^[OzUP[*r bWӠ}R 7 o{w۶ǂ^DT5tWnS~갿 EHI)S=ϛuD%߲-j^)@KiHlkHBU%[W#-#)@k٧M)=okRZOP^-9ȷ]MDJGT)HT?" iB7;ez" "G֤U(-/_wǼ{eA}S OI D%ޒ[bj[BcVR3QSB]v%Ҷ<"YYIc7.텪TGPT } W#t˃E,[ʇ{JeAU/EƟ#}])EL&P/T ꭃLw*jUPS2)&F/56+#ٴo[l˹EP/T m~x% ^)@"?ncS\/2D%/GV_P#P;Y˛8ɥ/M\0}oKLmKZLz.ے7n[@ HJیS˛RX?c^he|\Ҏ^^oVS2h:#RZY0^(EAPWvTAˬ*r "d$AU5 u  ;H鱲nhNH+Ŗ\@@LYP HHґRh+*J,%A}Oz-PJkDNNǛHMYp,. 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The keyword \"Subtitle\" will only work if no plot subtitle is used.") ) ), ## ARG 'SUMMARY.METHOD' NOT YET IMPLEMENTED ## # selectInput(inputId = "summary.method", # label = "Summary method", # selected = "unweighted", # choices = list("Unweighted" = "unweighted", # "Weighted" = "weighted", # "Monte Carlo" = "MCM")), # tooltip(refId = "summary.method", attr = "for", text = "Keyword indicating the method used to calculate the statistic summary. See calc_Statistics for details."), checkboxGroupInput(inputId = "stats", label = "Parameters", selected = c("n","mean"), choices = c("n" = "n", "Mean" = "mean", "Median" = "median", "rel. Standard deviation" = "sdrel", "abs. Standard deviation" = "sdabs", "rel. Standard error" = "serel", "abs. Standard error" = "seabs", "Skewness" = "skewness", "Kurtosis" = "kurtosis" # "% in 2 sigma range" = "in.2s" ) ), tooltip(refId = "stats", text = "Statistical parameters to be shown in the summary"), div(align = "center", h5("Error bars")), checkboxInput(inputId = "errorBars", label = "Show standard error points", value = TRUE), tooltip(refId = "errorBars", text = "Plot the standard error points over the histogram.") ),##EndOf::Tab_2 # Tab 1: Data input tabPanel("Plot", div(align = "center", h5("Title")), fluidRow( column(width = 6, textInput(inputId = "main", label = "Title", value = "Histogram") ), column(width = 6, textInput(inputId = "mtext", label = "Subtitle", value = "") ) ), div(align = "center", h5("Histogram bars")), fluidRow( column(width = 6, selectInput(inputId = "barsColor", label = "Bar color", selected = "grey80", choices = list("White" = "white", "Black" = "black", "Grey" = "grey80", "Red" = "#b22222", "Green" = "#6E8B3D", "Blue" = "#428bca", "Custom" = "custom")) ), column(width = 6, # show only if custom color is desired conditionalPanel(condition = "input.barsColor == 'custom'", jscolorInput(inputId = "barsRgb", label = "Choose a color")) ) ), sliderInput(inputId = "alpha.bars", label = "Bar transparency", min = 0, max = 100, step = 1, value = 66), br(), div(align = "center", h5("Normal curve")), checkboxInput(inputId = "norm", label = "Add normal curve", value = FALSE), tooltip(refId = "norm", text = "Add a normal curve to the histogram. Mean and standard deviation are calculated from the input data. If the normal curve is added, the y-axis in the histogram will show the probability density"), fluidRow( column(width = 6, selectInput(inputId = "normalColor", label = "Normal curve color", selected = "red", choices = list("Black" = "black", "Grey" = "grey50", "Red" = "#b22222", "Green" = "#6E8B3D", "Blue" = "#428bca", "Custom" = "custom")) ), column(width = 6, # show only if custom color is desired conditionalPanel(condition = "input.normalColor == 'custom'", jscolorInput(inputId = "normalRgb", label = "Choose a color")) ) ), div(align = "center", h5("Scaling")), sliderInput(inputId = "cex", label = "Scaling factor", min = 0.5, max = 2, value = 1.0, step = 0.1), br(), div(align = "center", h5("Rugs")), checkboxInput(inputId = "rugs", label = "Add rugs", value = TRUE), tooltip(refId = "rugs", text = "Option to add a rug to the KDE part, to indicate the location of individual values"), fluidRow( column(width = 6, selectInput(inputId = "rugsColor", label = "Rugs color", choices = list("Black" = "black", "Grey" = "grey50", "Red" = "#b22222", "Green" = "#6E8B3D", "Blue" = "#428bca", "Custom" = "custom")) ), column(width = 6, # show only if custom color is desired conditionalPanel(condition = "input.rugsColor == 'custom'", jscolorInput(inputId = "rugsRgb", label = "Choose a color")) ) ) ),##EndOf::Tab_9 # Tab 4: modify axis parameters tabPanel("Axis", div(align = "center", h5("X-axis")), textInput(inputId = "xlab", label = "Label x-axis", value = "Equivalent dose [Gy]"), # inject sliderInput from Server.R uiOutput(outputId = "xlim"), div(align = "center", h5("Y-axis")), fluidRow( column(width = 6, textInput(inputId = "ylab1", label = "Label y-axis (left)", value = "Counts") ), column(width = 6, textInput(inputId = "ylab2", label = "Label y-axis (right)", value = "Error") ) ) ),##EndOf::Tab_4 # Tab 5: modify data point representation tabPanel("Datapoints", div(align = "center", h5("Primary data set")), fluidRow( column(width = 6, selectInput(inputId = "pch", label = "Style", selected = "17", choices = c("Square"= "1", "Circle"="2", "Triangle point up"="3", "Plus"="4", "Cross"="5", "Diamond"="6", "Triangle point down"="7", "Square cross"="8", "Star"="9", "Diamond plus"="10", "Circle plus"="11", "Triangles up and down"="12", "Square plus"="13", "Circle cross"="14", "Square and Triangle down"="15", "filled Square"="16", "filled Circle"="17", "filled Triangle point up"="18", "filled Diamond"="19", "solid Circle"="20", "Bullet (smaller Circle)"="21", "Custom"="custom")) ), column(width = 6, # show only if custom symbol is desired conditionalPanel(condition = "input.pch == 'custom'", textInput(inputId = "custompch", label = "Insert character", value = "?")) ) ), fluidRow( column(width = 6, selectInput(inputId = "pchColor", label = "Datapoint color", choices = list("Black" = "black", "Grey" = "grey50", "Red" = "#b22222", "Green" = "#6E8B3D", "Blue" = "#428bca", "Custom" = "custom")) ), column(width = 6, # show only if custom color is desired conditionalPanel(condition = "input.pchColor == 'custom'", jscolorInput(inputId = "pchRgb", label = "Choose a color")) ) ) ),##EndOf::Tab_5 # Tab 9: save plot as pdf, wmf or eps tabPanel("Export", radioButtons(inputId = "fileformat", label = "Fileformat", selected = "pdf", choices = c("PDF (Portable Document Format)" = "pdf", "SVG (Scalable Vector Graphics)" = "svg", "EPS (Encapsulated Postscript)" = "eps")), textInput(inputId = "filename", label = "Filename", value = "Histogram"), fluidRow( column(width = 6, numericInput(inputId = "imgheight", label = "Image height", value = 7) ), column(width = 6, numericInput(inputId = "imgwidth", label = "Image width", value = 7) ) ), selectInput(inputId = "fontfamily", label = "Font", selected = "Helvetica", choices = c("Helvetica" = "Helvetica", "Helvetica Narrow" = "Helvetica Narrow", "Times" = "Times", "Courier" = "Courier", "Bookman" = "Bookman", "Palatino" = "Palatino")), tags$hr(), downloadButton(outputId = "exportFile", label = "Download plot"), tags$hr(), helpText("Additionally, you can download a corresponding .R file that contains", "a fully functional script to reproduce the plot in your R environment!"), downloadButton(outputId = "exportScript", label = "Download R script") ),##EndOf::Tab_8 # Tab 10: further information tabPanel("About", hr(), div(align = "center", # HTML code to include a .png file in the tab; the image file must be in # a subfolder called "wwww" img(src="RL_Logo.png", height = 100, width = 100, alt = "R.Lum"), p("Links:"), a(href = "http://www.r-luminescence.de", "R.Luminescence project page", target="_blank"), br(), a(href = "https://forum.r-luminescence.de", "Message board", target="_blank"), br(), a(href = "http://zerk.canopus.uberspace.de/R.Lum", "Online application", target="_blank"), br(),hr(), img(src='GitHub-Mark-32px.png', width='32px', height='32px'), br(), a(href = "https://github.com/tzerk/RLumShiny/tree/master/inst/shiny/histogram", "See the code at GitHub!", target="_blank") )#/div )##EndOf::Tab_9 )##EndOf::tabsetPanel ),##EndOf::sidebarPanel # 3 - output panel mainPanel(width = 7, # insert css code inside of the generated HTML file: # allow open dropdown menus to reach over the container tags$head(tags$style(type="text/css",".tab-content {overflow: visible;}")), tags$head(includeCSS("www/style.css")), # divide output in separate tabs via tabsetPanel tabsetPanel( tabPanel("Plot", plotOutput(outputId = "main_plot", height = "500px")), tabPanel("Data set", dataTableOutput("dataset")), tabPanel("Central Age Model", dataTableOutput("CAM")), tabPanel("R plot code", verbatimTextOutput("plotCode")) )###EndOf::tabsetPanel )##EndOf::mainPanel )##EndOf::shinyUI(pageWithSidebar)RLumShiny/inst/shiny/histogram/server.R0000644000176200001440000002255312743662035017720 0ustar liggesusers## Server.R library(Luminescence) library(shiny) # load example data data(ExampleData.DeValues) data <- ExampleData.DeValues$CA1 ## MAIN FUNCTION shinyServer(function(input, output, session) { # check and read in file (DATA SET 1) datGet<- reactive({ inFile<- input$file1 if(is.null(inFile)) return(NULL) # if no file was uploaded return NULL return(read.table(file = inFile$datapath, # inFile[1] contains filepath sep = input$sep, quote = "", header = input$headers)) # else return file }) # dynamically inject sliderInput for x-axis range output$xlim<- renderUI({ # check if file is loaded # # case 1: yes -> slinderInput with custom values if(!is.null(datGet())) { data<- datGet() xlim.plot<- range(hist(data[,1], plot = FALSE)$breaks) sliderInput(inputId = "xlim", label = "Range x-axis", min = xlim.plot[1]*0.5, max = xlim.plot[2]*1.5, value = c(xlim.plot[1], xlim.plot[2]), round=FALSE, step=0.0001) } else { #case 2: no -> sliderInput for example data xlim.plot<- range(hist(data[,1], plot = FALSE)$breaks) sliderInput(inputId = "xlim", label = "Range x-axis", min = xlim.plot[1]*0.5, max = xlim.plot[2]*1.5, value = c(xlim.plot[1], xlim.plot[2]), round=FALSE, step=0.0001) } })## EndOf::renderUI() output$main_plot <- renderPlot({ # refresh plot on button press input$refresh # progress bar progress<- Progress$new(session, min = 0, max = 3) progress$set(message = "Calculation in progress", detail = "Retrieve data") on.exit(progress$close()) # make sure that input panels are registered on non-active tabs. # by default tabs are suspended and input variables are hence # not available outputOptions(x = output, name = "xlim", suspendWhenHidden = FALSE) # check if file is loaded and overwrite example data if(!is.null(datGet())) { data<- datGet() } progress$set(value = 1) progress$set(message = "Calculation in progress", detail = "Get values") # check if any summary stats are activated, else NA if (input$summary) { summary<- input$stats } else { summary<- NA } # if custom datapoint color get RGB code from separate input panel if(input$pchColor == "custom") { pch.color<- input$pchRgb } else { pch.color<- input$pchColor } # if custom datapoint color get RGB code from separate input panel if(input$barsColor == "custom") { bars.color<- adjustcolor(col = input$barsRgb, alpha.f = input$alpha.bars/100) } else { bars.color<- adjustcolor(col = input$barsColor, alpha.f = input$alpha.bars/100) } # if custom datapoint color get RGB code from separate input panel if(input$rugsColor == "custom") { rugs.color<- input$rugsRgb } else { rugs.color<- input$rugsColor } # if custom datapoint color get RGB code from separate input panel if(input$normalColor == "custom") { normal.color<- input$normalRgb } else { normal.color<- input$normalColor } # update progress bar progress$set(value = 2) progress$set(message = "Calculation in progress", detail = "Combine values") colors<- c(bars.color, rugs.color, normal.color, pch.color) # if custom datapoint style get char from separate input panel if(input$pch == "custom") { pch<- input$custompch } else { pch<- as.integer(input$pch)-1 #-1 offset in pch values } # validate(need()) makes sure that all data are available to # renderUI({}) before plotting and will wait until there validate( need(expr = input$xlim, message = 'Waiting for data... Please wait!') ) progress$set(value = 3) progress$set(message = "Calculation in progress", detail = "Ready to plot") args <- list(data = data, na.rm = input$naExclude, cex.global = input$cex, pch = pch, xlim = input$xlim, summary.pos = input$sumpos, mtext = input$mtext, main = input$main, rug = input$rugs, se = input$errorBars, normal_curve = input$norm, summary = summary, xlab = input$xlab, ylab = c(input$ylab1, input$ylab2), colour = colors) do.call(plot_Histogram, args = args) # prepare code as text output if (is.null(input$sep)) updateRadioButtons(session, "fileformat", selected = "\t") if(input$sep == "\t") verb.sep<- "\\t" else verb.sep<- input$sep str1 <- paste("data <- read.delim(file, header = ",input$headers, ", sep= '", verb.sep,"')", sep = "") header <- paste("# To reproduce the plot in your local R environment", "# copy and run the following code to your R console.", "library(Luminescence)", "file<- file.choose()", str1, "\n", sep = "\n") names <- names(args) verb.arg <- paste(mapply(function(name, arg) { if (all(inherits(arg, "character"))) arg <- paste0("'", arg, "'") if (length(arg) > 1) arg <- paste0("c(", paste(arg, collapse = ", "), ")") if (is.null(arg)) arg <- "NULL" paste(name, "=", arg) }, names[-1], args[-1]), collapse = ",\n") funCall <- paste0("plot_Histogram(data = data,\n", verb.arg, ")") code.output <- paste0(header, funCall, collapse = "\n") # nested renderText({}) for code output on "R plot code" tab output$plotCode<- renderText({ code.output })##EndOf::renderText({}) output$exportScript <- downloadHandler( filename = function() { paste(input$filename, ".", "R", sep="") }, content = function(file) { write(code.output, file) },#EO content =, contentType = "text" )#EndOf::dowmloadHandler() # nested downloadHandler() to print plot to file output$exportFile <- downloadHandler( filename = function() { paste(input$filename, ".", input$fileformat, sep="") }, content = function(file) { # determine desired fileformat and set arguments if(input$fileformat == "pdf") { pdf(file, width = input$imgwidth, height = input$imgheight, paper = "special", useDingbats = FALSE, family = input$fontfamily) } if(input$fileformat == "svg") { svg(file, width = input$imgwidth, height = input$imgheight, family = input$fontfamily) } if(input$fileformat == "eps") { postscript(file, width = input$imgwidth, height = input$imgheight, paper = "special", family = input$fontfamily) } do.call(plot_Histogram, args = args) dev.off() },#EO content =, contentType = "image" )#EndOf::dowmloadHandler() })##EndOf::renderPlot({}) # renderTable() that prints the data to the second tab output$dataset<- renderDataTable( options = list(pageLength = 10, autoWidth = FALSE), callback = "function(table) { table.on('click.dt', 'tr', function() { $(this).toggleClass('selected'); Shiny.onInputChange('rows', table.rows('.selected').data().toArray()); }); }", { if(!is.null(datGet())) { data<- datGet() colnames(data)<- c("De","De error") data } else { colnames(data)<- c("De","De error") data } })##EndOf::renterTable() # reactive function for gVis plots that allow for dynamic input! myOptionsCAM<- reactive({ options<- list( page="enable", width="500px", sort="disable") return(options) }) # renderTable() to print the results of the # central age model (CAM) output$CAM<- renderDataTable( options = list(pageLength = 10, autoWidth = FALSE), { if(!is.null(datGet())) { data<- list(datGet()) } else { data<- list(data) } t<- as.data.frame(matrix(nrow = length(data), ncol = 7)) colnames(t)<- c("Data set","n", "log data", "Central dose", "SE abs.", "OD (%)", "OD error (%)") res<- lapply(data, function(x) { calc_CentralDose(x, verbose = FALSE, plot = FALSE) }) for(i in 1:length(res)) { t[i,1]<- ifelse(i==1,"pimary","secondary") t[i,2]<- length(res[[i]]@data$data[,1]) t[i,3]<- res[[i]]@data$args$log t[i,4:7]<- round(res[[i]]@data$summary[1:4],2) } t })##EndOf::renterTable() })##EndOf::shinyServer(function(input, output)RLumShiny/inst/shiny/histogram/www/0000755000176200001440000000000012743662035017104 5ustar liggesusersRLumShiny/inst/shiny/histogram/www/GitHub-Mark-32px.png0000644000176200001440000000326212743662035022461 0ustar liggesusersPNG  IHDR szztEXtSoftwareAdobe ImageReadyqe<$iTXtXML:com.adobe.xmp $IDATxėmhayL30A+R#f>IHکy(M)_o5 0+0Ėl&o{i^]u<{Yws}=uC>$L, }<w}8^ AO?p! 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"), jscolorInput(inputId = "jscol1")) ) ), br(), div(align = "center", h5("Scaling")), sliderInput(inputId = "cex", label = "Scaling factor", min = 0.5, max = 2, value = 1.0, step = 0.1) ),##EndOf::Tab_3 # Tab 4: modify axis parameters tabPanel("Axis", div(align = "center", h5("X-axis")), checkboxInput(inputId = "logx", label = "Logarithmic x-axis", value = TRUE), textInput(inputId = "xlab", label = "Label x-axis", value = "t [s]"), # inject sliderInput from Server.R br(), div(align = "center", h5("Y-axis")), checkboxInput(inputId = "logy", label = "Logarithmic y-axis", value = FALSE), textInput(inputId = "ylab", label = "Label y-axis (left)", value = "pseudo OSL [cts/s]") ),##EndOf::Tab_4 # Tab 10: save plot as pdf, wmf or eps tabPanel("Export", radioButtons(inputId = "fileformat", label = "Fileformat", selected = "pdf", choices = c("PDF (Portable Document Format)" = "pdf", "SVG (Scalable Vector Graphics)" = "svg", "EPS (Encapsulated Postscript)" = "eps")), textInput(inputId = "filename", label = "Filename", value = "transformed CW"), fluidRow( column(width = 6, numericInput(inputId = "imgheight", label = "Image height", value = 7) ), column(width = 6, numericInput(inputId = "imgwidth", label = "Image width", value = 7) ) ), selectInput(inputId = "fontfamily", label = "Font", selected = "Helvetica", choices = c("Helvetica" = "Helvetica", "Helvetica Narrow" = "Helvetica Narrow", "Times" = "Times", "Courier" = "Courier", "Bookman" = "Bookman", "Palatino" = "Palatino")), tags$hr(), downloadButton(outputId = "exportFile", label = "Download plot"), tags$hr(), helpText("The transformed CW curve data can be downloaded as a comma separated ASCII file."), downloadButton(outputId = "exportScript", label = "Download transformed data") ),##EndOf::Tab_8 # Tab 10: further information tabPanel("About", hr(), div(align = "center", # HTML code to include a .png file in the tab; the image file must be in # a subfolder called "wwww" img(src="RL_Logo.png", height = 100, width = 100, alt = "R.Lum"), p("Links:"), a(href = "http://www.r-luminescence.de", "R.Luminescence project page", target="_blank"), br(), a(href = "https://forum.r-luminescence.de", "Message board", target="_blank"), br(), a(href = "http://zerk.canopus.uberspace.de/R.Lum", "Online application", target="_blank"), br(),hr(), img(src='GitHub-Mark-32px.png', width='32px', height='32px'), br(), a(href = "https://github.com/tzerk/RLumShiny/tree/master/inst/shiny/transformCW", "See the code at GitHub!", target="_blank") )#/div )##EndOf::Tab_9 )##EndOf::tabsetPanel ),##EndOf::sidebarPanel # 3 - output panel mainPanel(width = 7, # insert css code inside of the generated HTML file: # allow open dropdown menus to reach over the container tags$head(tags$style(type="text/css",".tab-content {overflow: visible;}")), tags$head(includeCSS("www/style.css")), # divide output in separate tabs via tabsetPanel tabsetPanel( tabPanel("Plot", plotOutput(outputId = "main_plot", height = "500px")), tabPanel("Output table", fluidRow(column(width = 12, dataTableOutput("dataset")))) )###EndOf::tabsetPanel )##EndOf::mainPanel )##EndOf::shinyUI(pageWithSidebar)RLumShiny/inst/shiny/transformCW/Server.R0000644000176200001440000001017712743662035020127 0ustar liggesusers## Server.R library(Luminescence) library(RLumShiny) library(shiny) data("ExampleData.CW_OSL_Curve", envir = environment()) data <- ExampleData.CW_OSL_Curve ## MAIN FUNCTION shinyServer(function(input, output, session) { # RECEIVE USER DATA ---- datGet<- reactive({ inFile<- input$file if(is.null(inFile)) return(NULL) t <- tryCatch(read.table(file = inFile$datapath, sep = input$sep, quote = "", header = input$headers), error = function(e) { return(NULL) }) if (is.null(t)) return(NULL) if (ncol(t) == 1) return(NULL) return(t) }) # TRANSFORM DATA observe({ if (!is.null(datGet())) data <- datGet() P <- input$p delta <- input$delta # validate method parameters if (is.na(input$delta)) { updateNumericInput(session, "delta", value = 1) delta <- 1 } else if (input$delta < 1) { updateNumericInput(session, "delta", value = 1) delta <- 1 } # validate method parameters if (is.na(input$p)) { updateNumericInput(session, "p", value = 1) P <- 1 } else if (input$p < 1) { updateNumericInput(session, "p", value = 1) P <- 1 } args <- list(data) if (input$method == "CW2pHMi") if (delta >= 1) args <- append(args, delta) if (input$method == "CW2pLMi" || input$method == "CW2pPMi") if (P >= 1) args <- append(args, P) tdata <<- do.call(input$method, args) }) output$main_plot <- renderPlot({ # be reactive on method changes datGet() input$method input$delta input$p pargs <- list(tdata[ ,1], tdata[ ,2], log = paste0(ifelse(input$logx, "x", ""), ifelse(input$logy, "y", "")), main = input$main, xlab = input$xlab, ylab = input$ylab, cex = input$cex, type = input$type, pch = ifelse(input$pch != "custom", as.integer(input$pch) - 1, input$custompch), col = ifelse(input$color != "custom", input$color, input$jscol1)) do.call(plot, pargs) output$exportScript <- downloadHandler( filename = function() { paste(input$filename, ".", "txt", sep="") }, content = function(file) { write.table(tdata, file, sep = ",", quote = FALSE, row.names = FALSE) },#EO content =, contentType = "text" )#EndOf::dowmloadHandler() # nested downloadHandler() to print plot to file output$exportFile <- downloadHandler( filename = function() { paste(input$filename, ".", input$fileformat, sep="") }, content = function(file) { # determine desired fileformat and set arguments if(input$fileformat == "pdf") { pdf(file, width = input$imgwidth, height = input$imgheight, paper = "special", useDingbats = FALSE, family = input$fontfamily) } if(input$fileformat == "svg") { svg(file, width = input$imgwidth, height = input$imgheight, family = input$fontfamily) } if(input$fileformat == "eps") { postscript(file, width = input$imgwidth, height = input$imgheight, paper = "special", family = input$fontfamily) } # plot curve do.call(plot, args = pargs) dev.off() },#EO content =, contentType = "image" )#EndOf::dowmloadHandler() }) output$dataset <- renderDataTable({ # be reactive on method changes datGet() input$method input$delta input$p if (exists("tdata")){ tdata } }) })##EndOf::shinyServer(function(input, output)RLumShiny/NAMESPACE0000644000176200001440000000026212743662035013373 0ustar liggesusers# Generated by roxygen2: do not edit by hand export(app_RLum) export(jscolorInput) export(popover) export(tooltip) import(Luminescence) import(googleVis) import(shiny) RLumShiny/NEWS0000644000176200001440000000153312743662035012655 0ustar liggesusersRLumShiny 0.1.1 (Release date: 2016-07-20) ============== * New application to transform CW OSL curves (keyword 'transformCW') using the functions 'CW2pHMi', 'CW2pLM', 'CW2pLMi' and 'CW2pPMi' of the R package 'Luminescence'. * Removed UI elements that used now deprecated function arguments. * Added new UI elements for arguments added to functions after version 0.4.2 of the 'Luminescence' package. * Removed the database feature in the abanico plot application. * Removed dependencies on 'digest' and 'RCurl'. * Removed all 'Exit' buttons. * Code output to reproduce the plots is now generated dynamically and should be more reliable. * R Luminescence Package Team now properly mentioned as contributors. * Fixed many typos. RLumShiny 0.1.0 (Release date: 2015-03-31) ============== * Initial releaseRLumShiny/R/0000755000176200001440000000000012743662035012355 5ustar liggesusersRLumShiny/R/popover.R0000644000176200001440000000456612743662035014205 0ustar liggesusers#' Create a bootstrap button with popover #' #' Add small overlays of content for housing secondary information. #' #' @param title \code{\link{character}} (required): Title of the button. #' @param content \code{\link{character}}: Text to be displayed in the popover. #' @param header \code{\link{character}}: Optional header in the popover. #' @param html \code{\link{logical}} Insert HTML into the popover. #' @param class \code{\link{logical}} Bootstrap button class (e.g. "btn btn-danger"). #' @param placement \code{\link{character}}: How to position the popover - top | bottom | left | right | auto. When "auto" is specified, it will dynamically reorient the popover. For example, if placement is "auto left", the popover will display to the left when possible, otherwise it will display right. #' @param trigger \code{\link{character}}: How popover is triggered - click | hover | focus | manual. #' #' @examples #' # html code #' popover("title", "Some content") #' #' # example app #' \dontrun{ #' shinyApp( #' ui = fluidPage( #' jscolorInput(inputId = "col", label = "JSColor Picker", #' value = "21BF6B", position = "right", #' mode = "HVS", close = TRUE), #' popover(title = "Help!", content = "Call 911"), #' plotOutput("plot") #' ), #' server = function(input, output) { #' output$plot <- renderPlot({ #' plot(cars, col = input$col, cex = 2, pch = 16) #' }) #' }) #' } #' @import shiny #' @export popover <- function(title, content, header = NULL, html = TRUE, class = "btn btn-default", placement = c('right', 'top', 'left', 'bottom'), trigger = c('click', 'hover', 'focus', 'manual')) { tagList( singleton( tags$head( tags$script("$(function() { $(\"[data-toggle='popover']\").popover(); })") ) ), tags$a( tabindex = "0", href = NULL, role = "button", class = class, `data-toggle` = "popover", title = header, `data-content` = content, `data-animation` = TRUE, html = html, `data-placement` = match.arg(placement, several.ok=TRUE)[1], `data-trigger` = match.arg(trigger, several.ok=TRUE)[1], title ) ) } # helpPopup Button by Winston Chang from RStudio: # https://gist.github.com/jcheng5/5913297 # Documentation: http://getbootstrap.com/javascript/#popovers-usageRLumShiny/R/jscolor.R0000644000176200001440000000550412743662035014157 0ustar liggesusers#' Create a JSColor picker input widget #' #' Creates a JSColor (Javascript/HTML Color Picker) widget to be used in shiny applications. #' #' @param inputId \code{\link{character}} (required): Specifies the input slot that will be used to access the value. #' @param label \code{\link{character}}: Display label for the control, or NULL for no label. #' @param value \code{\link{character}}: Initial RGB value of the color picker. Default is black ('#000000'). #' @param position \code{\link{character}}: Position of the picker relative to the text input ('bottom', 'left', 'top', 'right'). #' @param color \code{\link{character}}: Picker color scheme ('transparent' by default). Use RGB color coding ('000000'). #' @param mode \code{\link{character}}: Mode of hue, saturation and value. Can either be 'HSV' or 'HVS'. #' @param slider \code{\link{logical}}: Show or hide the slider. #' @param close \code{\link{logical}}: Show or hide a close button. #' #' @seealso Other input.elements: \code{\link{animationOptions}}, \code{\link{sliderInput}}; #' \code{\link{checkboxGroupInput}}; \code{\link{checkboxInput}}; \code{\link{dateInput}}; #' \code{\link{dateRangeInput}}; \code{\link{fileInput}}; \code{\link{numericInput}}; #' \code{\link{passwordInput}}; \code{\link{radioButtons}}; \code{\link{selectInput}}, #' \code{\link{selectizeInput}}; \code{\link{submitButton}}; \code{\link{textInput}} #' #' @examples #' # html code #' jscolorInput("col", "Color", "21BF6B", slider = FALSE) #' #' # example app #' \dontrun{ #' shinyApp( #' ui = fluidPage( #' jscolorInput(inputId = "col", label = "JSColor Picker", #' value = "21BF6B", position = "right", #' mode = "HVS", close = TRUE), #' plotOutput("plot") #' ), #' server = function(input, output) { #' output$plot <- renderPlot({ #' plot(cars, col = input$col, cex = 2, pch = 16) #' }) #' }) #' } #' @import shiny #' @export jscolorInput <- function(inputId, label, value, position = 'bottom', color = 'transparent', mode = 'HSV', slider = TRUE, close = FALSE) { tagList( singleton(tags$head(tags$script(src = "RLumShiny/jscolor_inputBinding.js"))), singleton(tags$head(tags$script(src = "RLumShiny/jscolor/jscolor.js"))), if (missing(label)) { tags$p(" ") } else if (!is.null(label)) { tags$p(label) }, tags$input(id = inputId, value = ifelse(!missing(value), value, "#000000"), class = sprintf("color {hash:true, pickerPosition:'%s', pickerBorderColor:'transparent', pickerFaceColor:'%s', pickerMode:'%s', slider:%s, pickerClosable:%s} shiny-bound-input", position, color, mode, tolower(slider), tolower(close)), onchange = sprintf("$('#%s').trigger('afterChange')", inputId)), tags$script(sprintf("$('#%s').trigger('afterChange')", inputId)) ) }RLumShiny/R/app_RLum.R0000644000176200001440000000473312743662035014226 0ustar liggesusers#' Run Luminescence shiny apps #' #' A wrapper for \code{\link{runApp}} to start interactive shiny apps for the R package Luminescence. #' #' The RLumShiny package provides a single function from which all shiny apps can be started: \code{app_RLum()}. #' It essentially only takes one argument, which is a unique keyword specifying which application to start. #' See the table below for a list of available shiny apps and which keywords to use. #' #' \tabular{lcl}{ #' \bold{Application name:} \tab \bold{Keyword:} \tab \bold{Function:} \cr #' Abanico Plot \tab \emph{abanico} \tab \code{\link{plot_AbanicoPlot}} \cr #' Histogram \tab \emph{histogram} \tab \code{\link{plot_Histogram}} \cr #' Kernel Density Estimate Plot \tab \emph{KDE} \tab \code{\link{plot_KDE}} \cr #' Radial Plot \tab \emph{radialplot} \tab \code{\link{plot_RadialPlot}} \cr #' Dose Recovery Test \tab \emph{doserecovery} \tab \code{\link{plot_DRTResults}} \cr #' Cosmic Dose Rate \tab \emph{cosmicdose} \tab \code{\link{calc_CosmicDoseRate}} \cr #' CW Curve Transformation \tab \emph{transformCW} \tab \code{\link{CW2pHMi}, \link{CW2pLM}, \link{CW2pLMi}, \link{CW2pPMi}} #' } #' #' The \code{app_RLum()} function is just a wrapper for \code{\link{runApp}}. #' Via the \code{...} argument further arguments can be directly passed to \code{\link{runApp}}. #' See \code{?shiny::runApp} for further details on valid arguments. #' #' @param app \code{\link{character}} (required): name of the application to start. See details for a list #' of available apps. #' @param ... further arguments to pass to \code{\link{runApp}} #' @author Christoph Burow, University of Cologne (Germany) #' @seealso \code{\link{runApp}} #' @examples #' #' \dontrun{ #' # Plotting apps #' app_RLum("abanico") #' app_RLum("histogram") #' app_RLum("KDE") #' app_RLum("radialplot") #' app_RLum("doserecovery") #' #' # Further apps #' app_RLum("cosmicdose") #' } #' #' @export app_RLum app_RLum <- function(app, ...) { valid_apps <- c("abanico", "cosmicdose", "doserecovery", "histogram", "KDE", "radialplot", "transformCW") if (!app %in% valid_apps) return(message(paste0("Invalid app name: ", app, " \n Valid options are: ", paste(valid_apps, collapse = ", ")))) app <- shiny::runApp(system.file(paste0("shiny/", app), package = "RLumShiny"), launch.browser = TRUE, ...) }RLumShiny/R/tooltip.R0000644000176200001440000000571112743662035014176 0ustar liggesusers#' Create a bootstrap tooltip #' #' Create bootstrap tooltips for any HTML element to be used in shiny applications. #' #' @param refId \code{\link{character}} (required): id of the element the tooltip is to be attached to. #' @param text \code{\link{character}}: Text to be displayed in the tooltip. #' @param attr \code{\link{character}}: Attach tooltip to all elements with attribute \code{attr='refId'}. #' @param animation \code{\link{logical}}: Apply a CSS fade transition to the tooltip. #' @param delay \code{\link{numeric}}: Delay showing and hiding the tooltip (ms). #' @param html \code{\link{logical}}: Insert HTML into the tooltip. #' @param placement \code{\link{character}}: How to position the tooltip - top | bottom | left | right | auto. When 'auto' is specified, it will dynamically reorient the tooltip. For example, if placement is 'auto left', the tooltip will display to the left when possible, otherwise it will display right. #' @param trigger \code{\link{character}}: How tooltip is triggered - click | hover | focus | manual. You may pass multiple triggers; separate them with a space. #' #' @examples #' # javascript code #' tt <- tooltip("elementId", "This is a tooltip.") #' str(tt) #' #' # example app #' \dontrun{ #' shinyApp( #' ui = fluidPage( #' jscolorInput(inputId = "col", label = "JSColor Picker", #' value = "21BF6B", position = "right", #' mode = "HVS", close = TRUE), #' tooltip("col", "This is a JScolor widget"), #' #' checkboxInput("cbox", "Checkbox", FALSE), #' tooltip("cbox", "This is a checkbox"), #' #' checkboxGroupInput("cboxg", "Checkbox group", selected = "a", #' choices = c("a" = "a", #' "b" = "b", #' "c" = "c")), #' tooltip("cboxg", "This is a checkbox group", html = TRUE), #' #' selectInput("select", "Selectinput", selected = "a", choices = c("a"="a", "b"="b")), #' tooltip("select", "This is a text input field", attr = "for", placement = "right"), #' #' passwordInput("pwIn", "Passwordinput"), #' tooltip("pwIn", "This is a password input field"), #' #' plotOutput("plot") #' ), #' server = function(input, output) { #' output$plot <- renderPlot({ #' plot(cars, col = input$col, cex = 2, pch = 16) #' }) #' }) #' } #' @import shiny #' @export tooltip <- function(refId, text, attr = NULL, animation = TRUE, delay = 100, html = TRUE, placement = 'auto', trigger = 'hover') { if (is.null(attr)) el <- sprintf("'#%s'", refId) else el <- sprintf("\"[%s='%s']\"", attr, refId) tagList( tags$head(tags$script(HTML(sprintf("$(window).load(function(){ $(%s).tooltip({ html: %s, trigger: '%s', title: '%s', animation: %s, delay: {'show': %i, 'hide': %i}, placement: '%s' }); })", el, tolower(html), trigger, text, tolower(animation), delay, delay, placement)))) ) }RLumShiny/R/zzz.R0000644000176200001440000000056012743662035013336 0ustar liggesusers# add libraries to ressource path .onLoad <- function(libname, pkgname) { shiny::addResourcePath("RLumShiny", system.file("www", package = "RLumShiny")) } # Dependencies in the shiny apps are currently not registered by R CMD check --as-cran .satisfyCheck <- function() { x <- TRUE if (x) return(x) Luminescence::sTeve() googleVis::renderGvis() }RLumShiny/R/RLumShiny.R0000644000176200001440000000240712743662035014375 0ustar liggesusers#' Shiny Applications for the R Package Luminescence #' #' A collection of shiny applications for the R package Luminescence. #' These mainly, but not exclusively, include applications for plotting chronometric #' data from e.g. luminescence or radiocarbon dating. 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[aut, cre], R Luminescence Package Team [ctb], Jan Odvarko [cph] (jscolor.js in www/jscolor), AnalytixWare [cph] (ShinySky package) Authors@R: c( person("Christoph", "Burow", role = c("aut", "cre"), email = "christoph.burow@uni-koeln.de"), person(family = "R Luminescence Package Team", role = "ctb"), person("Jan", "Odvarko", role = "cph", comment = "jscolor.js in www/jscolor"), person(family = "AnalytixWare", role = "cph", comment = "ShinySky package" ) ) Maintainer: Christoph Burow Description: A collection of 'shiny' applications for the R package 'Luminescence'. These mainly, but not exclusively, include applications for plotting chronometric data from e.g. luminescence or radiocarbon dating. It further provides access to bootstraps tooltip and popover functionality and contains the 'jscolor.js' library with a custom 'shiny' output binding. License: GPL-3 Depends: R (>= 3.3.0) Imports: Luminescence (>= 0.6.1), shiny (>= 0.13.0), googleVis URL: https://github.com/tzerk/RLumShiny BugReports: https://github.com/tzerk/RLumShiny/issues Collate: 'app_RLum.R' 'jscolor.R' 'tooltip.R' 'popover.R' 'RLumShiny.R' 'zzz.R' RoxygenNote: 5.0.1 NeedsCompilation: no Packaged: 2016-07-20 11:44:33 UTC; C Repository: CRAN Date/Publication: 2016-07-20 17:49:32 RLumShiny/LICENSE.note0000644000176200001440000000061312743662035014125 0ustar liggesusersThe RLumShiny package as a whole is distributed under GPL-3 (GNU GENERAL PUBLIC LICENSE version 3). The RLumShiny package includes other open source software components. The following is a list of these components: - JSColor, https://github.com/odvarko/jscolor, GPLv3 License - ShinySky, https://github.com/AnalytixWare/ShinySky, MIT license (YEAR: 2015, COPYRIGHT HOLDER: AnalytixWare)RLumShiny/man/0000755000176200001440000000000012743662035012727 5ustar liggesusersRLumShiny/man/popover.Rd0000644000176200001440000000332512743662035014713 0ustar liggesusers% Generated by roxygen2: do not edit by hand % Please edit documentation in R/popover.R \name{popover} \alias{popover} \title{Create a bootstrap button with popover} \usage{ popover(title, content, header = NULL, html = TRUE, class = "btn btn-default", placement = c("right", "top", "left", "bottom"), trigger = c("click", "hover", "focus", "manual")) } \arguments{ \item{title}{\code{\link{character}} (required): Title of the button.} \item{content}{\code{\link{character}}: Text to be displayed in the popover.} \item{header}{\code{\link{character}}: Optional header in the popover.} \item{html}{\code{\link{logical}} Insert HTML into the popover.} \item{class}{\code{\link{logical}} Bootstrap button class (e.g. "btn btn-danger").} \item{placement}{\code{\link{character}}: How to position the popover - top | bottom | left | right | auto. When "auto" is specified, it will dynamically reorient the popover. For example, if placement is "auto left", the popover will display to the left when possible, otherwise it will display right.} \item{trigger}{\code{\link{character}}: How popover is triggered - click | hover | focus | manual.} } \description{ Add small overlays of content for housing secondary information. } \examples{ # html code popover("title", "Some content") # example app \dontrun{ shinyApp( ui = fluidPage( jscolorInput(inputId = "col", label = "JSColor Picker", value = "21BF6B", position = "right", mode = "HVS", close = TRUE), popover(title = "Help!", content = "Call 911"), plotOutput("plot") ), server = function(input, output) { output$plot <- renderPlot({ plot(cars, col = input$col, cex = 2, pch = 16) }) }) } } RLumShiny/man/app_RLum.Rd0000644000176200001440000000402412743662035014735 0ustar liggesusers% Generated by roxygen2: do not edit by hand % Please edit documentation in R/app_RLum.R \name{app_RLum} \alias{app_RLum} \title{Run Luminescence shiny apps} \usage{ app_RLum(app, ...) } \arguments{ \item{app}{\code{\link{character}} (required): name of the application to start. See details for a list of available apps.} \item{...}{further arguments to pass to \code{\link{runApp}}} } \description{ A wrapper for \code{\link{runApp}} to start interactive shiny apps for the R package Luminescence. } \details{ The RLumShiny package provides a single function from which all shiny apps can be started: \code{app_RLum()}. It essentially only takes one argument, which is a unique keyword specifying which application to start. See the table below for a list of available shiny apps and which keywords to use. \tabular{lcl}{ \bold{Application name:} \tab \bold{Keyword:} \tab \bold{Function:} \cr Abanico Plot \tab \emph{abanico} \tab \code{\link{plot_AbanicoPlot}} \cr Histogram \tab \emph{histogram} \tab \code{\link{plot_Histogram}} \cr Kernel Density Estimate Plot \tab \emph{KDE} \tab \code{\link{plot_KDE}} \cr Radial Plot \tab \emph{radialplot} \tab \code{\link{plot_RadialPlot}} \cr Dose Recovery Test \tab \emph{doserecovery} \tab \code{\link{plot_DRTResults}} \cr Cosmic Dose Rate \tab \emph{cosmicdose} \tab \code{\link{calc_CosmicDoseRate}} \cr CW Curve Transformation \tab \emph{transformCW} \tab \code{\link{CW2pHMi}, \link{CW2pLM}, \link{CW2pLMi}, \link{CW2pPMi}} } The \code{app_RLum()} function is just a wrapper for \code{\link{runApp}}. Via the \code{...} argument further arguments can be directly passed to \code{\link{runApp}}. See \code{?shiny::runApp} for further details on valid arguments. } \examples{ \dontrun{ # Plotting apps app_RLum("abanico") app_RLum("histogram") app_RLum("KDE") app_RLum("radialplot") app_RLum("doserecovery") # Further apps app_RLum("cosmicdose") } } \author{ Christoph Burow, University of Cologne (Germany) } \seealso{ \code{\link{runApp}} } RLumShiny/man/RLumShiny-package.Rd0000644000176200001440000000250012743662035016476 0ustar liggesusers% Generated by roxygen2: do not edit by hand % Please edit documentation in R/RLumShiny.R \docType{package} \name{RLumShiny-package} \alias{RLumShiny} \alias{RLumShiny-package} \title{Shiny Applications for the R Package Luminescence} \description{ A collection of shiny applications for the R package Luminescence. These mainly, but not exclusively, include applications for plotting chronometric data from e.g. luminescence or radiocarbon dating. It further provides access to bootstraps tooltip and popover functionality as well as a binding to JSColor. } \details{ In addition to its main purpose of providing convenient access to the Luminescence shiny applications (see \code{\link{app_RLum}}) this package also provides further functions to extend the functionality of shiny. From the Bootstrap framework the JavaScript tooltip and popover components can be added to any shiny application via \code{\link{tooltip}} and \code{\link{popover}}. It further provides a custom input binding to the JavaScript/HTML color picker JSColor. Offering access to most options provided by the JSColor API the function \code{\link{jscolorInput}} is easily implemented in a shiny app. RGB colors are returned as hex values and can be directly used in R's base plotting functions without the need of any format conversion. } RLumShiny/man/jscolorInput.Rd0000644000176200001440000000416212743662035015714 0ustar liggesusers% Generated by roxygen2: do not edit by hand % Please edit documentation in R/jscolor.R \name{jscolorInput} \alias{jscolorInput} \title{Create a JSColor picker input widget} \usage{ jscolorInput(inputId, label, value, position = "bottom", color = "transparent", mode = "HSV", slider = TRUE, close = FALSE) } \arguments{ \item{inputId}{\code{\link{character}} (required): Specifies the input slot that will be used to access the value.} \item{label}{\code{\link{character}}: Display label for the control, or NULL for no label.} \item{value}{\code{\link{character}}: Initial RGB value of the color picker. Default is black ('#000000').} \item{position}{\code{\link{character}}: Position of the picker relative to the text input ('bottom', 'left', 'top', 'right').} \item{color}{\code{\link{character}}: Picker color scheme ('transparent' by default). Use RGB color coding ('000000').} \item{mode}{\code{\link{character}}: Mode of hue, saturation and value. Can either be 'HSV' or 'HVS'.} \item{slider}{\code{\link{logical}}: Show or hide the slider.} \item{close}{\code{\link{logical}}: Show or hide a close button.} } \description{ Creates a JSColor (Javascript/HTML Color Picker) widget to be used in shiny applications. } \examples{ # html code jscolorInput("col", "Color", "21BF6B", slider = FALSE) # example app \dontrun{ shinyApp( ui = fluidPage( jscolorInput(inputId = "col", label = "JSColor Picker", value = "21BF6B", position = "right", mode = "HVS", close = TRUE), plotOutput("plot") ), server = function(input, output) { output$plot <- renderPlot({ plot(cars, col = input$col, cex = 2, pch = 16) }) }) } } \seealso{ Other input.elements: \code{\link{animationOptions}}, \code{\link{sliderInput}}; \code{\link{checkboxGroupInput}}; \code{\link{checkboxInput}}; \code{\link{dateInput}}; \code{\link{dateRangeInput}}; \code{\link{fileInput}}; \code{\link{numericInput}}; \code{\link{passwordInput}}; \code{\link{radioButtons}}; \code{\link{selectInput}}, \code{\link{selectizeInput}}; \code{\link{submitButton}}; \code{\link{textInput}} } RLumShiny/man/tooltip.Rd0000644000176200001440000000501512743662035014711 0ustar liggesusers% Generated by roxygen2: do not edit by hand % Please edit documentation in R/tooltip.R \name{tooltip} \alias{tooltip} \title{Create a bootstrap tooltip} \usage{ tooltip(refId, text, attr = NULL, animation = TRUE, delay = 100, html = TRUE, placement = "auto", trigger = "hover") } \arguments{ \item{refId}{\code{\link{character}} (required): id of the element the tooltip is to be attached to.} \item{text}{\code{\link{character}}: Text to be displayed in the tooltip.} \item{attr}{\code{\link{character}}: Attach tooltip to all elements with attribute \code{attr='refId'}.} \item{animation}{\code{\link{logical}}: Apply a CSS fade transition to the tooltip.} \item{delay}{\code{\link{numeric}}: Delay showing and hiding the tooltip (ms).} \item{html}{\code{\link{logical}}: Insert HTML into the tooltip.} \item{placement}{\code{\link{character}}: How to position the tooltip - top | bottom | left | right | auto. When 'auto' is specified, it will dynamically reorient the tooltip. For example, if placement is 'auto left', the tooltip will display to the left when possible, otherwise it will display right.} \item{trigger}{\code{\link{character}}: How tooltip is triggered - click | hover | focus | manual. You may pass multiple triggers; separate them with a space.} } \description{ Create bootstrap tooltips for any HTML element to be used in shiny applications. } \examples{ # javascript code tt <- tooltip("elementId", "This is a tooltip.") str(tt) # example app \dontrun{ shinyApp( ui = fluidPage( jscolorInput(inputId = "col", label = "JSColor Picker", value = "21BF6B", position = "right", mode = "HVS", close = TRUE), tooltip("col", "This is a JScolor widget"), checkboxInput("cbox", "Checkbox", FALSE), tooltip("cbox", "This is a checkbox"), checkboxGroupInput("cboxg", "Checkbox group", selected = "a", choices = c("a" = "a", "b" = "b", "c" = "c")), tooltip("cboxg", "This is a checkbox group", html = TRUE), selectInput("select", "Selectinput", selected = "a", choices = c("a"="a", "b"="b")), tooltip("select", "This is a text input field", attr = "for", placement = "right"), passwordInput("pwIn", "Passwordinput"), tooltip("pwIn", "This is a password input field"), plotOutput("plot") ), server = function(input, output) { output$plot <- renderPlot({ plot(cars, col = input$col, cex = 2, pch = 16) }) }) } }