Mod:

- trajectory plotting and cluster distribution plot turned into modules

global.R

 source('modules/auxfunc.R')
 source('modules/downPlot.R')
 source('modules/downCellIDsCls.R')
+source('modules/trajPlot.R')
+source('modules/clDistPlot.R')
 source('modules/tabScatter.R')
 source('modules/tabBoxPlot.R')
 source('modules/tabClBay.R')
\ No newline at end of file

modules/auxfunc.R

@@ -116,7 +116,7 @@ myGgplotTraj = function(dt.arg,
       aes_string(y = y.arg, group = 1),
       fun.data = mean_cl_normal,
       colour = 'red',
-      alpha = 0.5,
+      alpha = 0.25,
       geom = "ribbon",
       group = 1
     )
@@ -127,7 +127,7 @@ myGgplotTraj = function(dt.arg,
       aes_string(y = y.arg, group = 1),
       fun.data = mean_se,
       colour = 'red',
-      alpha = 0.5,
+      alpha = 0.25,
       geom = "ribbon",
       group = 1
     )
@@ -187,20 +187,23 @@ userDataGen <- function() {
   locNsites = 4
   locNwells = 1
   
-  x.rand.1 = c(rnorm(locNtp * locNtracks * locNsites * 0.5, 2, 0.5), rnorm(locNtp * locNtracks * locNsites * 0.5, 2, 0.5))
-  x.rand.2 = c(rnorm(locNtp * locNtracks * locNsites * 0.5, 0, 0.1), rnorm(locNtp * locNtracks * locNsites * 0.5, 0, 0.1))
-  x.rand.3 = rep(rnorm(locNtracks, 2, 0.5), 1, each = locNtp)
-  x.rand.4 = rep(rnorm(locNtracks, 1, 0.1), 1, each = locNtp)
+  x.rand.1 = c(rnorm(locNtp * locNtracks * locNsites * 0.5, .5, 0.1), rnorm(locNtp * locNtracks * locNsites * 0.5, 1, 0.2))
+  x.rand.2 = c(rnorm(locNtp * locNtracks * locNsites * 0.5, 0.25, 0.1), rnorm(locNtp * locNtracks * locNsites * 0.5, 0.5, 0.2))
+#  x.rand.3 = rep(rnorm(locNtracks, 2, 0.5), 1, each = locNtp)
+#  x.rand.4 = rep(rnorm(locNtracks, 1, 0.1), 1, each = locNtp)
   
-  x.arg = rep(seq(0, locNtp-1) / locNtp * 4 * pi, locNtracks * locNsites)
+#  x.arg = rep(seq(0, locNtp-1) / locNtp * 4 * pi, locNtracks * locNsites)
+  x.arg = rep(seq(1, locNtp), locNtracks * locNsites)
   
   dt.nuc = data.table(Metadata_Site = rep(1:locNsites, each = locNtp * locNtracks),
                       Metadata_Well = rep(1:locNwells, each = locNtp * locNsites * locNtracks / locNwells),
                       Metadata_RealTime = x.arg,
-#                      objCyto_Intensity_MeanIntensity_imErkCor = c(rnorm(locNtp * locNtracks * locNsites * 0.5, .5, 0.1), rnorm(locNtp * locNtracks * locNsites * 0.5, 1, 0.2)),
+                      objCyto_Intensity_MeanIntensity_imErkCor = x.rand.1,
+                      objNuc_Intensity_MeanIntensity_imErkCor  = x.rand.2,
+                      objNuc_Location_X = runif(locNtp * locNtracks * locNsites, min = 0, max = 1),
+                      objNuc_Location_Y = runif(locNtp * locNtracks * locNsites, min = 0, max = 1),
+#                      objCyto_Intensity_MeanIntensity_imErkCor = x.rand.3 + ifelse(x.arg < 4, 0, 1) / x.rand.3,
 #                      objNuc_Intensity_MeanIntensity_imErkCor  = c(rnorm(locNtp * locNtracks * locNsites * 0.5, .25, 0.1), rnorm(locNtp * locNtracks * locNsites * 0.5, .5, 0.2)),
-                      objCyto_Intensity_MeanIntensity_imErkCor = x.rand.3 + ifelse(x.arg < 4, 0, 1) / x.rand.3,
-                      objNuc_Intensity_MeanIntensity_imErkCor  = c(rnorm(locNtp * locNtracks * locNsites * 0.5, .25, 0.1), rnorm(locNtp * locNtracks * locNsites * 0.5, .5, 0.2)),
                       TrackLabel = rep(1:(locNtracks*locNsites), each = locNtp))
   
   cat(colnames(dt.nuc))

modules/clDistPlot.R

+modClDistPlotUI =  function(id, label = "Plot Fractions WIthin Clusters") {
+  ns <- NS(id)
+  
+  tagList(
+    actionButton(ns('butPlotClDist'), 'Plot!'),
+    plotOutput(ns('outPlotClDist'), height = '800px', width = 'auto'),
+    downPlotUI(ns('downPlotClDist'), "Download PDF")
+  )
+}
+
+
+modClDistPlot = function(input, output, session, in.data, in.fname = 'clDist.pdf') {
+  
+  ns <- session$ns
+ 
+  # Barplot with distribution of clusters across conditions
+  plotClDist = function() {
+    cat(file = stderr(), 'plotClDist: in\n')
+    
+    loc.dt = in.data()
+    if (is.null(loc.dt)) {
+      cat(file = stderr(), 'plotClDist: dt is NULL\n')
+      return(NULL)
+    }
+    
+    p.out = ggplot(loc.dt, aes(x = group, y = nCells)) +
+      geom_bar(aes(fill = as.factor(cl)), stat = 'identity', position = 'fill') +
+      scale_y_continuous(labels = percent) +
+      ylab("percentage of cells\n") +  
+      xlab("") +  
+      scale_fill_discrete(name = "Cluster no.") +
+      myGgplotTheme
+    
+    return(p.out)
+    
+  }
+  
+  #  Hierarchical - display bar plot
+  output$outPlotClDist <- renderPlot({
+    locBut = input$butPlotClDist
+    
+    if (locBut == 0) {
+      cat(file = stderr(), 'outPlotClDist: Go button not pressed\n')
+      
+      return(NULL)
+    }
+    
+    plotClDist()
+  })
+  
+  # Hierarchical - Bar Plot - download pdf
+  callModule(downPlot, "downPlotClDist", in.fname, plotClDist, TRUE)
+  
+}
\ No newline at end of file

modules/clHeatmapPlot.R

+modClDistPlotUI =  function(id, label = "Plot Fractions WIthin Clusters") {
+  ns <- NS(id)
+  
+}
+
+
+modClDistPlot = function(input, output, session, in.data, in.facet = 'group') {
+  
+  ns <- session$ns
+  
+}
\ No newline at end of file

modules/trajPlot.R

+modTrajPlotUI =  function(id, label = "Plot Individual Time Series") {
+  ns <- NS(id)
+  
+  tagList(
+    fluidRow(
+      column(
+        3,
+        numericInput(
+          ns('inPlotTrajFacetNcol'),
+          '#Columns:',
+          value = 4,
+          min = 1,
+          width = '100px',
+          step = 1
+        ),
+        checkboxInput(ns('chBplotTrajInt'), 'Interactive Plot?'),
+        actionButton(ns('butPlotTraj'), 'Plot!')
+      ),
+      column(
+        3,
+        checkboxGroupInput(ns('chBPlotTrajStat'), 'Stats:', list('Mean' = 'mean', '95% conf. interv.' = 'CI', 'Std. error' = 'SE'))
+      ),
+      column(
+        3,
+        sliderInput(ns('sliPlotTrajSkip'), 'Plot every n-th point:', min = 1, max = 10, value = 1, step = 1)
+      ),
+      column(
+        3,
+        numericInput(
+          ns('inPlotTrajWidth'),
+          'Width [%]:',
+          value = 100,
+          min = 10,
+          max = 100,
+          width = '100px',
+          step = 10
+        ),
+        numericInput(
+          ns('inPlotTrajHeight'),
+          'Height [px]:',
+          value = 800,
+          min = 100,
+          width = '100px',
+          step = 50
+        )
+      )
+    ),
+    uiOutput(ns('uiPlotTraj')),
+    downPlotUI(ns('downPlotTraj'), "Download PDF")
+  )
+}
+
+
+modTrajPlot = function(input, output, session, in.data, in.facet = 'group', in.fname = 'tCourses.pdf') {
+  
+  ns <- session$ns
+  
+  output$uiPlotTraj = renderUI({
+    if (input$chBplotTrajInt)
+      plotlyOutput(
+        ns("outPlotTrajInt"),
+        width = paste0(input$inPlotTrajWidth, '%'),
+        height = paste0(input$inPlotTrajHeight, 'px')
+      ) else
+        plotOutput(
+          ns("outPlotTraj"),
+          width = paste0(input$inPlotTrajWidth, '%'),
+          height = paste0(input$inPlotTrajHeight, 'px')
+        )
+  })
+  
+  output$outPlotTraj <- renderPlot({
+    
+    loc.p = plotTraj()
+    if(is.null(loc.p))
+      return(NULL)
+    
+    return(loc.p)
+  })
+  
+  
+  output$outPlotTrajInt <- renderPlotly({
+    # This is required to avoid
+    # "Warning: Error in <Anonymous>: cannot open file 'Rplots.pdf'"
+    # When running on a server. Based on:
+    # https://github.com/ropensci/plotly/issues/494
+    if (names(dev.cur()) != "null device")
+      dev.off()
+    pdf(NULL)
+    
+    loc.p = plotTraj()
+    if(is.null(loc.p))
+      return(NULL)
+    
+    return(plotly_build(loc.p))
+  })
+  
+  
+  
+  # Trajectory plot - download pdf
+  callModule(downPlot, "downPlotTraj", in.fname, plotTraj, TRUE)
+  
+  plotTraj <- function() {
+    cat(file = stderr(), 'plotTraj: in\n')
+    locBut = input$butPlotTraj
+    
+    if (locBut == 0) {
+      cat(file = stderr(), 'plotTraj: Go button not pressed\n')
+      
+      return(NULL)
+    }
+    
+    loc.dt = isolate(in.data())
+    
+    cat("plotTraj: on to plot\n\n")
+    if (is.null(loc.dt)) {
+      cat(file = stderr(), 'plotTraj: dt is NULL\n')
+      return(NULL)
+    }
+    
+    cat(file = stderr(), 'plotTraj: dt not NULL\n')
+    
+    
+    # Future: change such that a column with colouring status is chosen by the user
+    # colour trajectories, if dataset contains mi.din column
+    # with filtering status of trajectory
+    if (sum(names(loc.dt) %in% 'mid.in') > 0)
+      loc.line.col.arg = 'mid.in'
+    else
+      loc.line.col.arg = NULL
+    
+    # select every other point for plotting
+    loc.dt = loc.dt[, .SD[seq(1, .N, input$sliPlotTrajSkip)], by = id]
+    
+    # check if columns with XY positions are present
+    if (sum(names(loc.dt) %like% 'pos') == 2)
+      locPos = TRUE
+    else
+      locPos = FALSE
+    
+    p.out = myGgplotTraj(
+      dt.arg = loc.dt,
+      x.arg = 'realtime',
+      y.arg = 'y',
+      group.arg = "id",
+      facet.arg = in.facet,
+      facet.ncol.arg = input$inPlotTrajFacetNcol,
+      xlab.arg = 'Time (min)',
+      line.col.arg = loc.line.col.arg,
+      aux.label1 = if (locPos) 'pos.x' else NULL,
+      aux.label2 = if (locPos) 'pos.y' else NULL,
+      stat.arg = input$chBPlotTrajStat
+    )
+    
+    return(p.out)
+  }
+}
\ No newline at end of file

ui.R

@@ -77,49 +77,9 @@ shinyUI(fluidPage(
         checkboxInput('chBhighlightTraj', 'Highlight trajectories?', FALSE),
         uiOutput('varSelHighlight'),
         br(),
-        fluidRow(
-          column(
-            4,
-            numericInput(
-              'inPlotTrajFacetNcol',
-              '#Columns:',
-              value = 4,
-              min = 1,
-              width = '100px',
-              step = 1
-            ),
-            checkboxInput('chBplotTrajInt', 'Interactive Plot?'),
-            actionButton('butPlotTraj', 'Plot!')
-          ),
-          column(
-            4,
-            sliderInput('sliPlotTrajSkip', 'Plot every n-th point:', min = 1, max = 10, value = 1, step = 1),
-            checkboxGroupInput('chBPlotTrajStat', 'Stats:', list('Mean' = 'mean', '95% conf. interv.' = 'CI', 'Std. error' = 'SE'))
-          ),
-          column(
-            4,
-            numericInput(
-              'inPlotTrajWidth',
-              'Width [%]:',
-              value = 100,
-              min = 10,
-              max = 100,
-              width = '100px',
-              step = 10
-            ),
-            numericInput(
-              'inPlotTrajHeight',
-              'Height [px]:',
-              value = 800,
-              min = 100,
-              width = '100px',
-              step = 50
-            )
-          )
+        modTrajPlotUI('modTrajPlot')
         ),
-        uiOutput('uiPlotTraj'),
-        downPlotUI('downPlotTraj', "Download PDF")
-      ),
+      
       
       tabPanel(
         "Box-plots",
@@ -272,13 +232,11 @@ shinyUI(fluidPage(
           # tabPanel('Heat-map int.',
           #          helpText("Choose your settings 2")),
           tabPanel('Time-courses',
-                   actionButton('butPlotHierTraj', 'Plot!'),
-                   plotOutput('outPlotHierTraj' , height = '800px', width = 'auto'),
-                   downPlotUI('downPlotHierTraj', "Download PDF")),
+                   modTrajPlotUI('modPlotHierTraj')),
+          
           tabPanel('Cluster dist.',
-                   actionButton('butPlotHierClDist', 'Plot!'),
-                   plotOutput('outPlotHierClDist', height = '800px', width = 'auto'),
-                   downPlotUI('downPlotHierClDist', "Download PDF"))
+                   modClDistPlotUI('hierClDistPlot', 'xxx'))
+          
         )
       ),
       
@@ -452,13 +410,9 @@ shinyUI(fluidPage(
           # tabPanel('Heat-map int.',
           #          helpText("Choose your settings 2")),
           tabPanel('Time-courses',
-                   actionButton('butPlotHierSparTraj', 'Plot!'),
-                   plotOutput('outPlotHierSparTraj', height = '800px', width = 'auto'),
-                   downPlotUI('downPlotHierSparTraj', "Download PDF")),
+                   modTrajPlotUI('modPlotHierSparTraj')),
           tabPanel('Cluster dist.',
-                   actionButton('butPlotHierSparClDist', 'Plot!'),
-                   plotOutput('outPlotHierSparClDist', height = '800px', width = 'auto'),
-                   downPlotUI('downPlotHierSparClDist', "Download PDF"))
+                   modClDistPlotUI('hierClSparDistPlot'))
         )
       )
       #