--- a/barplot.r	Sun Mar 24 18:23:00 2019 -0400
+++ b/barplot.r	Mon Oct 07 08:40:41 2019 -0400
@@ -12,6 +12,7 @@
 library(optparse)
 library(ggplot2)
 library(ggrepel)
+library(RColorBrewer)
 
 
 #Arguments
@@ -39,12 +40,24 @@
 colnames(annotations) = c("sample", "class", "percent_of_reads", "total")
 annotations$percent=round(annotations$percent_of_reads/annotations$total*100, digits=2)
 # ggplot2 plotting
+
+# Define the number of colors you want
+Sasha.Trubetskoy.Palette <- c('#e6194b', '#3cb44b', '#ffe119', '#4363d8', '#f58231',
+                              '#911eb4', '#46f0f0', '#f032e6', '#bcf60c',
+                              '#008080', '#e6beff', '#9a6324', '#fffac8', '#800000',
+                              '#aaffc3', '#808000', '#ffd8b1', '#000075', '#808080')
+nb.cols <- 19  # 10 with colorRampPalette
+# mycolors <- colorRampPalette(brewer.pal(8, "Paired"))(nb.cols)
+mycolors <- Sasha.Trubetskoy.Palette[1:nb.cols]
+
 ggtitle('Class proportions') 
 ggplot(annotations, aes(x=total/2, y = percent_of_reads, fill = class, width = total)) +
        geom_bar(position="fill", stat="identity") + 
-       facet_wrap(~sample, ncol=3 ) + geom_label_repel(aes(label = percent), position = position_fill(vjust = 0.5), size=2,show.legend = F) +
+       facet_wrap(~sample, ncol=3 ) +
+       geom_label_repel(aes(label = percent), position = position_fill(vjust = 0.5), size=2,show.legend = F) +
        coord_polar(theta="y") +
        labs(x = "Class fractions (%)") +
+       scale_fill_manual(values = mycolors) +
        theme(axis.text = element_blank(),
              axis.ticks = element_blank(),
              panel.grid  = element_blank(),