Added multiple columns for facetting

auxfunc.R

@@ -36,9 +36,7 @@ myGgplotTraj = function(dt.arg,
                         plotlab.arg = NULL,
                         dt.stim.arg = NULL,
                         tfreq.arg = 1,
-                        maxrt.arg = 60,
-                        xaxisbreaks.arg = 10,
-                        ylim.arg = c(0,1),
+                        ylim.arg = NULL,
                         stim.bar.height.arg = 0.1,
                         stim.bar.width.arg = 0.5) {
   p.tmp = ggplot(dt.arg,
@@ -75,9 +73,10 @@ myGgplotTraj = function(dt.arg,
                                  group = 1) 
   }
   
+  if (!is.null(ylim.arg)) 
+    p.tmp = p.tmp + coord_cartesian(ylim = ylim.arg)
+  
   p.tmp = p.tmp + 
-    scale_x_continuous(breaks = seq(0, maxrt.arg, xaxisbreaks.arg)) +
-    coord_cartesian(ylim = ylim.arg) +
     xlab(paste0(xlab.arg, "\n")) +
     ylab(paste0("\n", ylab.arg)) +
     ggtitle(plotlab.arg) +

server.R

@@ -14,7 +14,7 @@ library(plotly)
 options(shiny.maxRequestSize=30*1024^2)
 source('auxfunc.R')
 
-shinyServer(function(input, output) {
+shinyServer(function(input, output, session) {
   
   butCounter <- reactiveValues(
     dataLoadNuc  = isolate(ifelse(is.null(input$inFileNucLoad), 0, 1)), 
@@ -34,7 +34,7 @@ shinyServer(function(input, output) {
     locColSel = locCols[locCols %like% 'ite'][1] # index 1 at the end in case more matches; select 1st
 
     cat(locColSel, '\n')
-    selectInput('inSelSite', 'Select Grouping (e.g. Metadata_Site or Well):', locCols, width = '100%', selected = locColSel)
+    selectInput('inSelSite', 'Select FOV (e.g. Metadata_Site or Metadata_Series):', locCols, width = '100%', selected = locColSel)
   })
   
   output$varSelTrackLabel = renderUI({
@@ -52,30 +52,86 @@ shinyServer(function(input, output) {
     locColSel = locCols[locCols %like% 'ime'][1] # index 1 at the end in case more matches; select 1st
     
     cat(locColSel, '\n')
-    selectInput('inSelTime', 'Select Time (e.g. RealTime):', locCols, width = '100%', selected = locColSel)
+    selectInput('inSelTime', 'Select X (e.g. RealTime):', locCols, width = '100%', selected = locColSel)
   })
 
-    output$varSelMeas1 = renderUI({
-    cat(file=stderr(), 'UI varSelMeas1\n')
+  # This is main field to select plot facet grouping
+  # It's typically a column with the entire experimental description,
+  # e.g. in Yannick's case it's Stim_All_Ch or Stim_All_S.
+  # In Coralie's case it's a combination of 3 columns called Stimulation_...
+  output$varSelGroup = renderUI({
+    cat(file=stderr(), 'UI varSelGroup\n')
     locCols = getDataNucCols()
-    locColSel = locCols[locCols %like% 'MeanIntensity'][1] # index 1 at the end in case more matches; select 1st
+    locColSel = locCols[locCols %like% 'timulation']
+    if (length(locColSel) == 0)
+      locColSel = locCols[locCols %like% 'ite'][1] # index 1 at the end in case more matches; select 1st
+    else if (length(locColSel) > 1) {
+      locColSel = locColSel[1]      
+    }
     
-    cat(locColSel, '\n')
-    selectInput('inSelMeas1', 'Select 1st Measurement:', locCols, width = '100%', selected = locColSel)
+#    cat('UI varSelGroup::locColSel ', locColSel, '\n')
+    selectInput('inSelGroup', 'Select Grouping for Plotting (e.g. Site, Well, Channel):', locCols, width = '100%', selected = locColSel)
   })
 
-  output$varSelRatio = renderUI({
-    cat(file=stderr(), 'UI varSelRatio\n')
-    checkboxInput('inSelRatio', 'Divide by:', 0)
+  output$varSelGroup2 = renderUI({
+    cat(file=stderr(), 'UI varSelGroup2\n')
+    locCols = getDataNucCols()
+    locColSel = locCols[locCols %like% 'timulation']
+    if (length(locColSel) == 0)
+      locColSel = locCols[locCols %like% 'ite'][1] # index 1 at the end in case more matches; select 1st
+    else if (length(locColSel) > 1) {
+#      updateCheckboxInput(session, 'inGroupMore1', value = 1)
+      locColSel = locColSel[2]      
+    }
+    
+#    cat('UI varSelGroup2::locColSel ', locColSel, '\n')
+    
+
+    if(input$inGroupMore1) {
+      selectInput('inSelGroup2', 'Select Additional Grouping:', locCols, width = '100%', selected = locColSel)
+    } else {
+      disabled(selectInput('inSelGroup2', 'Select Additional Grouping:', locCols, width = '100%', selected = locColSel))
+    }
+  })
+  
+  output$varSelGroup3 = renderUI({
+    cat(file=stderr(), 'UI varSelGroup2\n')
+    locCols = getDataNucCols()
+    locColSel = locCols[locCols %like% 'timulation']
+    if (length(locColSel) == 0)
+      locColSel = locCols[locCols %like% 'ite'][1] # index 1 at the end in case more matches; select 1st
+    else if (length(locColSel) > 1) {
+ #     updateCheckboxInput(session, 'inGroupMore2', value = 1)
+      locColSel = locColSel[3]      
+    }
+    
+#    cat('UI varSelGroup3::locColSel ', locColSel, '\n')
+    
+    
+    if(input$inGroupMore2) {
+      selectInput('inSelGroup3', 'Select Additional Grouping:', locCols, width = '100%', selected = locColSel)
+    } else {
+      disabled(selectInput('inSelGroup3', 'Select Additional Grouping:', locCols, width = '100%', selected = locColSel))
+    }
+  })
+  
+  output$varSelMeas1 = renderUI({
+    cat(file=stderr(), 'UI varSelMeas1\n')
+    locCols = getDataNucCols()
+    locColSel = locCols[locCols %like% 'Intensity'][1] # index 1 at the end in case more matches; select 1st
+    
+#    cat(locColSel, '\n')
+    selectInput('inSelMeas1', 'Select Y:', locCols, width = '100%', selected = locColSel)
   })
 
+
   output$varSelMeas2 = renderUI({
     cat(file=stderr(), 'UI varSelMeas2\n')
     locCols = getDataNucCols()
     locColSel = locCols[locCols %like% 'Intensity'][1] # index 1 at the end in case more matches; select 1st
     
-    cat(locColSel, '\n')
-    selectInput('inSelMeas2', 'Select 2nd Measurement:', locCols, width = '100%', selected = locColSel)
+#    cat(locColSel, '\n')
+    selectInput('inSelMeas2', 'Select 2nd operand:', locCols, width = '100%', selected = locColSel)
   })
   
   output$outPlot = renderUI({
@@ -98,7 +154,6 @@ shinyServer(function(input, output) {
     # make unique cell identifier based on metadata.site
     cat(file=stderr(), 'userDataNucMod: in\n')
     
-#    dt = userDataNuc()
     dt = dataInBoth()
     colNameSite  = input$inSelSite
     colNameTrackLabel = input$inSelTrackLabel
@@ -113,20 +168,6 @@ shinyServer(function(input, output) {
                                        sep = "_")]
 
     loc.colnames = colnames(dt)
-    if (sum(loc.colnames %like% 'Stimulation') == 0) {
-      dt[, metadata.site.stim := get(colNameSite)]
-    } else {
-      dt[, metadata.site.stim := paste(
-        sprintf('%02d', get(colNameSite)),
-        ': ',
-        Stimulation_duration,
-        ' ',
-        Stimulation_intensity,
-        ' ',
-        Stimulation_treatment,
-        sep = ''
-      )]
-    }
     
     cat(file=stderr(), 'userDataNucMod: out\n')
     return(dt)
@@ -146,26 +187,35 @@ shinyServer(function(input, output) {
   observeEvent(input$butReset, {
     reset("inFileNucLoad")  # reset is a shinyjs function
     reset("inFileStimLoad")  # reset is a shinyjs function
+
+    reset("inGroupMore1")  # reset is a shinyjs function
+    reset("inGroupMore2")  # reset is a shinyjs function
   })
   
   dataInBoth <- reactive({
     cat(file=stderr(), 'dataInBoth: in\n')
     
     locInGen = input$butDataGen
-    locInLoadNuc  = ifelse(is.null(input$inFileNucLoad),  0, isolate(butCounter$dataLoadNuc) + 1)
-    locInLoadStim = ifelse(is.null(input$inFileStimLoad), 0, isolate(butCounter$dataLoadStim) + 1)
+    locButLoadNuc = isolate(butCounter$dataLoadNuc)
+    locButLoadStim = isolate(butCounter$dataLoadStim)
+    locButGen = isolate(butCounter$dataGen)
+    cat("butCounter$dataGen: ", locButGen, "\nbutCounter$dataLoadNuc: ", locButLoadNuc, "\nbutCounter$locButLoadStim: ", locButLoadStim, "\n")
+    
+    locInLoadNuc  = ifelse(is.null(input$inFileNucLoad),  0, locButLoadNuc + 1)
+    locInLoadStim = ifelse(is.null(input$inFileStimLoad), 0, locButLoadStim + 1)
+    cat(file=stderr(), "dataInBoth\ninGen: ", locInGen, "\ninLoadNuc: ", locInLoadNuc, "\ninLoadStim: ", locInLoadStim, "\n")
     
-    cat(file=stderr(), "dataInBoth\n1: ", locInGen, "\n2: ", locInLoadNuc, "\n3: ", locInLoadStim, "\n")
     
     # isolate the checks of counter reactiveValues
     # as we set the values in this same reactive
-    if (locInLoadNuc != isolate(butCounter$dataLoadNuc)) {
+    if (locInLoadNuc != locButLoadNuc) {
       cat(file=stderr(), "dataInBoth if inFileNucLoad\n")
       dm = userDataNuc()
 
       # no need to isolate updating the counter reactive values!
+      
       butCounter$dataLoad <- locInLoadNuc
-    } else if (locInGen != isolate(butCounter$dataGen)) {
+    } else if (locInGen != locButGen) {
       cat(file=stderr(), "dataInBoth if inDataGen\n")
       dm = userDataGen()
       cat(colnames(dm))
@@ -189,9 +239,10 @@ shinyServer(function(input, output) {
     }
     
     
-    dt.nuc = (userDataNucMod())
+    dt.nuc = userDataNucMod()
     locInLoadStim = isolate(input$inFileStimLoad)
     
+    
     if (is.null(dt.nuc) && is.null(locInLoadStim)) {
       cat(file=stderr(), 'trajPlot: Data not yet loaded\n')
       
@@ -210,29 +261,35 @@ shinyServer(function(input, output) {
     loc.time = isolate(input$inSelTime)
     loc.meas.1 = isolate(input$inSelMeas1)
     
-    if (isolate(input$inSelRatio)) {
+    # create an expression for faceting (max 3 fields)
+    loc.facet.group = isolate(input$inSelGroup)
+    if (isolate(input$inGroupMore1)) {
+      loc.facet.group = paste0(loc.facet.group, ' + ', isolate(input$inSelGroup2))
+    } 
+    if (isolate(input$inGroupMore2)) {
+      loc.facet.group = paste0(loc.facet.group, ' + ', isolate(input$inSelGroup3))
+    }
+#    cat("loc.facet.group: ", loc.facet.group, "\n")
+    
+    
+    # create expression for plotting Y-axis
+    loc.math = isolate(input$inSelMath)
+    if (loc.math != '') {
       loc.meas.2 = isolate(input$inSelMeas2)
-      loc.y.arg = paste0(loc.meas.1, ' / ', loc.meas.2)
+      loc.y.arg = paste0(loc.meas.1, loc.math, loc.meas.2)
     }  else
       loc.y.arg = loc.meas.1
-    
-    cat(loc.y.arg)
+#    cat("loc.y.arg", loc.y.arg, "\n")
     
     p.out = myGgplotTraj(
       dt.arg = dt.nuc,
       x.arg = loc.time,
       y.arg = loc.y.arg,
       group.arg = "trackObjectsLabelUni",
-      facet.arg = 'metadata.site.stim',
-#      xlab.arg = "Time (min)",
-#      ylab.arg = loc.y.arg,
-#      plotlab.arg = "Raw data from illumination-corrected images",
+      facet.arg = loc.facet.group,
       dt.stim.arg = dt.stim,
       tfreq.arg = 1,
-      maxrt.arg = 120,
-      xaxisbreaks.arg = 10,
       facet.ncol.arg = loc.facet.ncol.arg,
-      ylim.arg = c(0, 1.2),
       stim.bar.height.arg = 0.05,
       stim.bar.width.arg = 1
     )
@@ -240,10 +297,22 @@ shinyServer(function(input, output) {
     #ggplotly(p.out)
     cat(file=stderr(), 'trajPlot: out\n')
     
+    # This is required to avoid 
+    # "Warning: Error in <Anonymous>: cannot open file 'Rplots.pdf'"
+    # When running on a server. Based on:
+    # https://github.com/ropensci/plotly/issues/494
     if (names(dev.cur()) != "null device") dev.off()
     pdf(NULL)
     
-    return(ggplotly(p.out))
+    p.out.ly = plotly_build(p.out)
+    
+    # Custom tooltip
+    # p.out.ly$x$data[[1]]$text <- sprintf("t: %d <br>y: %.2f <br>id: %s <br>s: %s", 
+    #                                      dt.nuc[[loc.time]], 
+    #                                      dt.nuc[[loc.y.arg]], dt.nuc[['trackObjectsLabelUni']],
+    #                                      dt.nuc[[loc.facet.group]])
+    
+    return(p.out.ly)
   })
   
 })

ui.R

@@ -31,23 +31,40 @@ shinyUI(fluidPage(
              accept = c('text/csv', 'text/comma-separated-values,text/plain')
            ),
            
+           h4("Plot format"),
+           fluidRow(
+             column(4, 
+                    numericInput('inFacetNcol', '#Columns:', value = 4, min = 1, width = '100px', step = 1)),
+             column(4, 
+                    numericInput('inPlotHeight', 'Height [px]:', value = 800, min = 100, width = '100px', step = 50)),
+             column(4, 
+                    numericInput('inPlotWidth', 'Width [%]:', value = 100, min = 10, max = 100, width = '100px', step = 10))
+           ),
+           
            actionButton("butReset", "Reset file input"),
            actionButton('butDataGen', 'Generate artificial dataset'),
            actionButton('butGo', 'Go!')),
     
-    column(4, offset = 1,
+    column(3, offset = 1,
            uiOutput('varSelSite'),
            uiOutput('varSelTrackLabel'),
            uiOutput('varSelTime'),
            uiOutput('varSelMeas1'),
            uiOutput('varSelRatio'),
+           radioButtons('inSelMath', 'Math operation 1st and 2nd meas.:', c('None' = '', 
+                                                                            'Divide' = " / ", 
+                                                                            'Sum' = " + ", 
+                                                                            'Multiply' = " * ", 
+                                                                            'Subtract' = ' - ')),
            uiOutput('varSelMeas2')),
   
-    column(2, offset = 1,
-           numericInput('inFacetNcol', 'No. of plot columns:', value = 4, min = 1, width = '150px', step = 1),
-           numericInput('inPlotHeight', 'Plot Height [px]:', value = 400, min = 100, width = '150px', step = 50),
-           numericInput('inPlotWidth', 'Plot Width [%]:', value = 100, min = 10, max = 100, width = '150px', step = 10))
-  ),
+    column(3, offset = 1,
+           uiOutput('varSelGroup'),
+           checkboxInput('inGroupMore1', 'More grouping?'),
+           uiOutput('varSelGroup2'),
+           checkboxInput('inGroupMore2', 'More grouping?'),
+           uiOutput('varSelGroup3'))
+),
   br(),
   uiOutput('outPlot')
 ))