Removed: option to manually assign cluster colours.

Various bug fixes.

modules/auxfunc.R

@@ -18,7 +18,7 @@ require(Hmisc) # for CI calculation
 # if true, additional output printed to R console
 DEB = T
 
-# font sizes in pts for plots
+# font sizes in pts for plots in the manuscript
 # PLOTFONTBASE = 8
 # PLOTFONTAXISTEXT = 8
 # PLOTFONTAXISTITLE = 8

modules/boxPlot.R

@@ -245,7 +245,8 @@ modBoxPlot = function(input, output, session,
                      in.font.strip = PLOTFONTFACETSTRIP, 
                      in.font.legend = PLOTFONTLEGEND) + 
       theme(legend.position = input$selPlotBoxLegendPos,
-            axis.text.x = LOCrotatedAxisElementText(as.numeric(input$rBAxisLabelsRotate)))
+            axis.text.x = LOCrotatedAxisElementText(as.numeric(input$rBAxisLabelsRotate), 
+                                                    size = PLOTFONTAXISTEXT))
 
     
     return(p.out)

modules/clDistPlot.R

@@ -63,7 +63,8 @@ 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$rBAxisLabelsRotate), size = PLOTFONTAXISTEXT)
+        axis.text.x = LOCrotatedAxisElementText(as.numeric(input$rBAxisLabelsRotate), 
+                                                size = PLOTFONTAXISTEXT)
     )
 
     return(p.out)

modules/tabClHier.R

@@ -51,8 +51,9 @@ clustHierUI <- function(id, label = "Hierarchical CLustering") {
                ticks = TRUE,
                round = TRUE
              ),
-             checkboxInput(ns('chBPlotHierClAss'), 'Manually assign cluster colours'),
-             uiOutput(ns('uiPlotHierClAss')),
+             # These two lines are to manually assign colours to clusters; it doesn't really work well, so skip
+             #checkboxInput(ns('chBPlotHierClAss'), 'Manually assign cluster colours'),
+             #uiOutput(ns('uiPlotHierClAss')),
              checkboxInput(ns('chBPlotHierClSel'), 'Manually select clusters to display'),
              uiOutput(ns('uiPlotHierClSel')),
              downloadButton(ns('downCellCl'), 'Download CSV with cell IDs and cluster no.')