Bug fixes in UI

modules/auxfunc.R

@@ -25,15 +25,22 @@ DEB = T
 # PLOTFONTFACETSTRIP = 10
 # PLOTFONTLEGEND = 8
 
-PLOTFONTBASE = 12
-PLOTFONTAXISTEXT = 12
-PLOTFONTAXISTITLE = 12
-PLOTFONTFACETSTRIP = 16
-PLOTFONTLEGEND = 12
-
+PLOTFONTBASE = 16
+PLOTFONTAXISTEXT = 16
+PLOTFONTAXISTITLE = 16
+PLOTFONTFACETSTRIP = 20
+PLOTFONTLEGEND = 16
+
+# height (in pixels) of ribbon and single traj. plots
+PLOTRIBBONHEIGHT = 500 # in pixels
+PLOTTRAJHEIGHT = 500 # in pixels
+PLOTPSDHEIGHT = 500 # in pixels
+PLOTBOXHEIGHT = 500 # in pixels
+PLOTSCATTERHEIGHT = 500 # in pixels
+PLOTWIDTH = 85 # in percent
 
 # default number of facets in plots
-PLOTNFACETDEFAULT = 2
+PLOTNFACETDEFAULT = 3
 
 # internal column names
 COLRT   = 'realtime'
@@ -499,7 +506,7 @@ LOCrotatedAxisElementText = function(angle, position='x', size = 12){
   rads = (-angle - positions[[ position ]])*pi/180
   hjust = round((1 - sin(rads)))/2
   vjust = round((1 + cos(rads)))/2
-  element_text(size = 12, angle = angle, vjust = vjust, hjust = hjust)
+  element_text(size = size, angle = angle, vjust = vjust, hjust = hjust)
 }
 
 # Plot individual time series

modules/boxPlot.R

@@ -43,7 +43,7 @@ modBoxPlotUI =  function(id, label = "Plot Box-plots") {
         numericInput(
           ns('inPlotBoxWidth'),
           'Width [%]:',
-          value = 100,
+          value = PLOTWIDTH,
           min = 10,
           width = '100px',
           step = 10
@@ -51,7 +51,7 @@ modBoxPlotUI =  function(id, label = "Plot Box-plots") {
         numericInput(
           ns('inPlotBoxHeight'),
           'Height [px]:',
-          value = 800,
+          value = PLOTBOXHEIGHT,
           min = 100,
           width = '100px',
           step = 50

modules/clDistPlot.R

@@ -7,7 +7,7 @@ modClDistPlotUI =  function(id, label = "Plot Fractions WIthin Clusters") {
                    "45 deg" = 45,
                    "90 deg" = 90)),
     actionButton(ns('butPlotClDist'), 'Plot!'),
-    plotOutput(ns('outPlotClDist'), height = '800px', width = 'auto'),
+    plotOutput(ns('outPlotClDist'), height = PLOTBOXHEIGHT, width = 'auto'),
     downPlotUI(ns('downPlotClDist'), "Download PDF")
   )
 }
@@ -63,7 +63,7 @@ modClDistPlot = function(input, output, session, in.data, in.cols = NULL, in.fna
                      in.font.strip = PLOTFONTFACETSTRIP, 
                      in.font.legend = PLOTFONTLEGEND) + 
       theme(
-        axis.text.x = LOCrotatedAxisElementText(as.numeric(input$rBAxisLabelsRotate))
+        axis.text.x = LOCrotatedAxisElementText(as.numeric(input$rBAxisLabelsRotate), size = PLOTFONTAXISTEXT)
     )
 
     return(p.out)

modules/clHeatmapPlot.R

-modHeatmapPlotUI =  function(id, label = "Plot Heatmap") {
-  ns <- NS(id)
-  
-}
-
-
-modHeatmapPlot = function(input, output, session, in.data) {
-  
-  ns <- session$ns
-  
-}
\ No newline at end of file

modules/selOutliers.R

@@ -67,7 +67,7 @@ modSelOutliers = function(input, output, session, in.data) {
   output$txtOutliersPerc <- renderText({ 
     cat(file = stdout(), 'modSelOutliers: txtOutliersPerc\n')
     
-      sprintf('<b>%d total track(s)<br>%d outlier track(s)<br>%d outlier point(s)</b><br>', 
+      sprintf('<b>%d total track(s)<br>%d removed track(s)<br>%d removed point(s)</b><br>', 
             nCellsCounter[['nCellsOrig']], 
             nCellsCounter[['nCellsOrig']] - nCellsCounter[['nCellsAfter']],
             nCellsCounter[['nOutlierTpts']])

modules/tabScatter.R

@@ -41,7 +41,7 @@ tabScatterPlotUI <- function(id, label = "Comparing t-points") {
         numericInput(
           ns('inPlotHeight'),
           'Display plot height [px]',
-          value = 1000,
+          value = PLOTSCATTERHEIGHT,
           min = 100,
           step = 100
         ),

modules/trajPlot.R

@@ -16,7 +16,7 @@ modTrajPlotUI =  function(id, label = "Plot Individual Time Series") {
   tagList(
     fluidRow(
       column(
-        3,
+        2,
         numericInput(
           ns('inPlotTrajFacetNcol'),
           '#Columns:',
@@ -29,7 +29,7 @@ modTrajPlotUI =  function(id, label = "Plot Individual Time Series") {
         actionButton(ns('butPlotTraj'), 'Plot!')
       ),
       column(
-        3,
+        2,
         checkboxGroupInput(ns('chBPlotTrajStat'), 'Stats:', list('Mean' = 'mean', '95% conf. interv.' = 'CI', 'Std. error' = 'SE'))
       ),
       column(
@@ -48,20 +48,19 @@ modTrajPlotUI =  function(id, label = "Plot Individual Time Series") {
         
       ),
       column(
-        3,
+        2,
         numericInput(
           ns('inPlotTrajWidth'),
           'Width [%]:',
-          value = 100,
+          value = PLOTWIDTH,
           min = 10,
-          max = 100,
           width = '100px',
           step = 10
         ),
         numericInput(
           ns('inPlotTrajHeight'),
           'Height [px]:',
-          value = 800,
+          value = PLOTTRAJHEIGHT,
           min = 100,
           width = '100px',
           step = 50

modules/trajPsdPlot.R

@@ -8,36 +8,43 @@ modPSDPlotUI =  function(id, label = "Plot PSD of average trajectory.") {
   tagList(
     fluidRow(
       column(
-        3,
+        2,
         radioButtons(ns('rBPSDmethod'), 'Method for PSD estimation:', list('Smoothed Fourier' = 'pgram', 'AR Fit' = 'ar')),
         checkboxInput(ns('chBplotTrajInt'), 'Interactive Plot'),
         actionButton(ns('butPlotTraj'), 'Plot!')
       ),
       column(
-        3,
+        2,
         selectInput(ns('inPSDxchoice'), 'X-axis:', list('Period'= TRUE, 'Frequency'= FALSE)),
         numericInput(ns('ninPSDsamplFreq'), '# time units between 2 points:', value = 1, min = 0, step = 1)
       ),
       column(
-        3,
-        selectInput(ns('inPSDlogtype'), 'Transformation:', list('1/x'='inverse_trans', 'log2'= 'log2', 'log10'= 'log10', 'ln'= 'log')),
-        checkboxGroupInput(ns('chBGPSDlogaxis'), 'Transform the axis:', list('x' = 'x', 'y' = 'y'), inline = TRUE)
+        2,
+        selectInput(ns('inPSDtransXtype'), 'Transform X-axis:', list('none' = 'none',
+                                                                   '1/x'='inverse_trans', 
+                                                                   'log2'= 'log2', 
+                                                                   'log10'= 'log10', 
+                                                                   'ln'= 'log')),
+        selectInput(ns('inPSDtransYtype'), 'Transform Y-axis:', list('none' = 'none',
+                                                                   '1/y'='inverse_trans', 
+                                                                   'log2'= 'log2', 
+                                                                   'log10'= 'log10', 
+                                                                   'ln'= 'log'))
       ),
       column(
-        3,
+        2,
         numericInput(
           ns('inPlotTrajWidth'),
           'Width [%]:',
           value = 100,
           min = 10,
-          max = 100,
           width = '100px',
           step = 10
         ),
         numericInput(
           ns('inPlotTrajHeight'),
           'Height [px]:',
-          value = 800,
+          value = PLOTPSDHEIGHT,
           min = 100,
           width = '100px',
           step = 50
@@ -205,24 +212,24 @@ modPSDPlot = function(input, output, session,
                      in.font.axis.title = PLOTFONTAXISTITLE, 
                      in.font.strip = PLOTFONTFACETSTRIP, 
                      in.font.legend = PLOTFONTLEGEND)
+
     # TODO: Restore tick labels when using inverse transformation
     # See: https://stackoverflow.com/questions/56130614/ggplot2-missing-labels-after-custom-scaling-of-axis
     inverse_trans <- scales::trans_new("myinverse", transform = function(x) 1/x,
                                        inverse = function(x) 1/(1/x))
-    if("x" %in% input$chBGPSDlogaxis){
-      if(input$inPSDlogtype == "inverse_trans"){
-        p.out <- p.out + scale_x_continuous(trans = inverse_trans)
-      } else {
-        p.out <- p.out + scale_x_continuous(trans = input$inPSDlogtype)
-      }
+    
+    if(input$inPSDtransXtype == "inverse_trans"){
+      p.out <- p.out + scale_x_continuous(trans = inverse_trans)
+    } else if (!(input$inPSDtransXtype == "none")) {
+      p.out <- p.out + scale_x_continuous(trans = input$inPSDtransXtype)
     }
-    if("y" %in% input$chBGPSDlogaxis){
-      if(input$inPSDlogtype == "inverse_trans"){
-        p.out <- p.out + scale_y_continuous(trans = inverse_trans)
-      } else {
-      p.out <- p.out + scale_y_continuous(trans = input$inPSDlogtype)
-      }
+    
+    if(input$inPSDtransYtype == "inverse_trans"){
+      p.out <- p.out + scale_y_continuous(trans = inverse_trans)
+    } else if (!(input$inPSDtransYtype == "none")) {
+      p.out <- p.out + scale_y_continuous(trans = input$inPSDtransYtype)
     }
+    
     return(p.out)
   }
 }
\ No newline at end of file

modules/trajRibbonPlot.R

@@ -6,7 +6,7 @@ modTrajRibbonPlotUI =  function(id, label = "Plot Individual Time Series") {
   tagList(
     fluidRow(
       column(
-        3,
+        2,
         checkboxInput(ns('chBplotTrajInt'), 'Interactive Plot'),
         radioButtons(ns('rBlegendPos'), 'Legend placement:', list('top' = 'top', 'right' = 'right')),
         actionButton(ns('butPlotTraj'), 'Plot!')
@@ -16,20 +16,19 @@ modTrajRibbonPlotUI =  function(id, label = "Plot Individual Time Series") {
         sliderInput(ns('sliPlotTrajSkip'), 'Plot every n-th point:', min = 1, max = 10, value = 1, step = 1)
       ),
       column(
-        3,
+        2,
         numericInput(
           ns('inPlotTrajWidth'),
           'Width [%]:',
-          value = 100,
+          value = PLOTWIDTH,
           min = 10,
-          max = 100,
           width = '100px',
           step = 10
         ),
         numericInput(
           ns('inPlotTrajHeight'),
           'Height [px]:',
-          value = 800,
+          value = PLOTRIBBONHEIGHT,
           min = 100,
           width = '100px',
           step = 50

ui.R

@@ -18,7 +18,7 @@ shinyUI(fluidPage(
   title = "Timecourse Inspector",
   
   sidebarLayout(
-    sidebarPanel(
+    sidebarPanel(width = 3,
       #Selector for file upload
       fileInput(
         'inFileLoadNuc',