Bug fixes: sparse clustering removed temporarily because sparcl unavailable on CRAN

modules/auxfunc.R

@@ -170,6 +170,26 @@ getClCol <- function(in.dend, in.k) {
 #####
 ## Common plotting functions
 
+myGgplotTheme = 
+  theme_bw(base_size = 8, base_family = "Helvetica") +
+  theme(
+    panel.spacing = unit(1, "lines"),
+    panel.grid.minor = element_blank(),
+    panel.grid.major = element_blank(),
+    panel.border = element_blank(),
+    axis.line.x = element_line(color = "black", size = 0.25),
+    axis.line.y = element_line(color = "black", size = 0.25),
+    axis.text = element_text(size = 8),
+    axis.title = element_text(size = 8),
+    strip.text = element_text(size = 10, face = "bold"),
+    strip.background = element_blank(),
+    legend.key = element_blank(), 
+    legend.text = element_text(size = 8),
+    legend.key.height = unit(1, "lines"),
+    legend.key.width = unit(2, "lines"),
+    legend.position = "top"
+  )
+
 myGgplotTraj = function(dt.arg, # data table
                         x.arg,  # string with column name for x-axis
                         y.arg, # string with column name for y-axis

modules/boxPlot.R

@@ -236,7 +236,8 @@ modBoxPlot = function(input, output, session,
       scale_fill_discrete(name = '') +
       xlab('') +
       ylab('') +
-      ggplotTheme() + 
+      #ggplotTheme() + 
+      myGgplotTheme + 
       theme(legend.position = input$selPlotBoxLegendPos)
     
     if (input$chBxAxisLabelsRotate)

modules/clDistPlot.R

@@ -50,6 +50,7 @@ modClDistPlot = function(input, output, session, in.data, in.cols = NULL, in.fna
       ylab("percentage of cells\n") +  
       xlab("") +  
       ggplotTheme()
+      #myGgplotTheme
     
     return(p.out)
     

modules/trajRibbonPlot.R

@@ -188,6 +188,7 @@ modTrajRibbonPlot = function(input, output, session,
                            xlab.arg = 'Time (min)',
                            ylab.arg = '') +
       ggplotTheme() +
+      #myGgplotTheme +
       theme(legend.position = input$rBlegendPos)
     
     return(p.out)

server.R

@@ -17,7 +17,8 @@ library(d3heatmap) # for interactive heatmap
 library(dendextend) # for color_branches
 library(colorspace) # for palettes (used to colour dendrogram)
 library(RColorBrewer)
-library(sparcl) # sparse hierarchical and k-means
+# sparcl temporarily unavailable on CRAN
+#library(sparcl) # sparse hierarchical and k-means
 library(scales) # for percentages on y scale
 library(dtw) # for dynamic time warping
 library(imputeTS) # for interpolating NAs

ui.R

@@ -142,12 +142,13 @@ shinyUI(fluidPage(
         tabPanel(
           'Hierarchical',
           clustHierUI('tabClHier')
-        ),
-        
-        tabPanel(
-          'Hierarchical Sparse',
-          clustHierSparUI('tabClHierSpar')
         )
+        
+        # sparse hierarchical clustering package sparcl temporarily unavailable from CRAN
+        # tabPanel(
+        #   'Hierarchical Sparse',
+        #   clustHierSparUI('tabClHierSpar')
+        #)
       ))
   )
 ))
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