Merge pull request #6 from majpark21/master

Changed default palette to colorblind friendly

modules/distPlot.R

@@ -274,9 +274,17 @@ modDistPlot = function(input, output, session,
         else
           NA
       ) 
+
+    
+    # If more than max.col groups, cycle through the palette ("Color Blind" can return 10 colors at maximum)
+    loc.pal = "Color Blind"
+    max.col = attr(ggthemes::tableau_color_pal(loc.pal), "max_n")
+    loc.col = ggthemes::tableau_color_pal(loc.pal)(n = max.col)
+    ngroups = uniqueN(loc.dt[, get(in.cols$group)]) - 1
+    loc.col = rep(loc.col, (ngroups %/% max.col) + 1)
+    loc.col = loc.col[1:(ngroups+1)]
     
     p.out = p.out +
-      scale_fill_discrete(name = in.labels$legend) +
       xlab(in.labels$x) +
       ylab(in.labels$y) +
       LOCggplotTheme(in.font.base = PLOTFONTBASE, 
@@ -286,7 +294,8 @@ modDistPlot = function(input, output, session,
                      in.font.legend = PLOTFONTLEGEND) + 
       theme(legend.position = input$selPlotBoxLegendPos,
             axis.text.x = LOCrotatedAxisElementText(as.numeric(input$rBAxisLabelsRotate), 
-                                                    size = PLOTFONTAXISTEXT))
+                                                    size = PLOTFONTAXISTEXT)) +
+      scale_fill_manual(name = in.labels$legend, values = loc.col)
     
     
     return(p.out)

modules/tabClValid.R

@@ -318,6 +318,9 @@ clustValid <- function(input, output, session, in.dataWide) {
     if (sum(is.na(loc.dm)) > 0)
       return(NULL)
     
+    loc.pal = ifelse(returnNclust() <= 10, "Color Blind", "Tableau 20")
+    loc.col = ggthemes::tableau_color_pal(loc.pal)(n = returnNclust())
+    
     loc.p = factoextra::fviz_cluster(loc.part, 
                                      data = loc.dm,
                                      geom = "point",
@@ -328,7 +331,9 @@ clustValid <- function(input, output, session, in.dataWide) {
                      in.font.axis.text = PLOTFONTAXISTEXT, 
                      in.font.axis.title = PLOTFONTAXISTITLE, 
                      in.font.strip = PLOTFONTFACETSTRIP, 
-                     in.font.legend = PLOTFONTLEGEND)
+                     in.font.legend = PLOTFONTLEGEND) +
+      scale_fill_manual(values = loc.col) +
+      scale_colour_manual(values = loc.col)
 
     
     # Retrieve association of cluster and colours and use it for dendrogram for color matching between dend, silhouette and PCA plot
@@ -396,6 +401,9 @@ clustValid <- function(input, output, session, in.dataWide) {
       need(!is.null(loc.part), "Nothing to plot. Load data first!")
     )    
     
+    loc.pal = ifelse(returnNclust() <= 10, "Color Blind", "Tableau 20")
+    loc.col = ggthemes::tableau_color_pal(loc.pal)(n = returnNclust())
+    
     loc.p = factoextra::fviz_silhouette(loc.part, 
                                         print.summary = FALSE, 
                                         main = "Silhouette") +
@@ -405,7 +413,9 @@ clustValid <- function(input, output, session, in.dataWide) {
                      in.font.axis.title = PLOTFONTAXISTITLE, 
                      in.font.strip = PLOTFONTFACETSTRIP, 
                      in.font.legend = PLOTFONTLEGEND) +
-      theme(axis.text.x = element_blank())
+      theme(axis.text.x = element_blank()) +
+      scale_fill_manual(values = loc.col) +
+      scale_colour_manual(values = loc.col)
     
     return(loc.p)
   }

modules/trajRibbonPlot.R

@@ -350,6 +350,14 @@ modTrajRibbonPlot = function(input, output, session,
       loc.ylim.arg = c(input$inSetYboundsLow, input$inSetYboundsHigh)
     } 
     
+    # If more than max.col groups, cycle through the palette ("Color Blind" can return 10 colors at maximum)
+    loc.pal = "Color Blind"
+    max.col = attr(ggthemes::tableau_color_pal(loc.pal), "max_n")
+    loc.col = ggthemes::tableau_color_pal(loc.pal)(n = max.col)
+    ngroups = uniqueN(loc.dt.aggr[, ..in.facet]) - 1
+    loc.col = rep(loc.col, (ngroups %/% max.col) + 1)
+    loc.col = loc.col[1:(ngroups+1)]
+    
     p.out = LOCplotTrajRibbon(dt.arg = loc.dt.aggr, 
                            x.arg = COLRT, 
                            y.arg = 'Mean',
@@ -368,7 +376,8 @@ modTrajRibbonPlot = function(input, output, session,
                      in.font.axis.title = PLOTFONTAXISTITLE, 
                      in.font.strip = PLOTFONTFACETSTRIP, 
                      in.font.legend = PLOTFONTLEGEND) + 
-      theme(legend.position = input$rBlegendPos)
+      theme(legend.position = input$rBlegendPos) +
+      scale_colour_manual(values = loc.col)
     
     return(p.out)
   }