Merge pull request #31 from galaxyproteomics/newpal

switch to scico pallette
galaxyproteomics · Apr 10, 2019 · 722cf30 · 722cf30
2 parents ec40470 + 9e5f8a4
commit 722cf30
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diff --git a/dev_environment.yml b/dev_environment.yml
@@ -15,5 +15,6 @@ dependencies:
 - r-gplots==3.0.*
 - r-ggplot2==3.0.*
 - r-base==3.5.1
+- r-scico=1.1.0
 - r-jsonlite=1.5.*
 - libiconv 1.15.*
diff --git a/metaquantome/modules/viz.R b/metaquantome/modules/viz.R
@@ -218,9 +218,8 @@ hclust.ward <- function(x) {
 }
 
 
-# from brewer.pal(name = 'PuBu', n = 9)
-heatmap_colors <- c("#FFF7FB", "#ECE7F2", "#D0D1E6", "#A6BDDB", "#74A9CF",
-                    "#3690C0", "#0570B0", "#045A8D", "#023858")
+library(scico)
+heatmap_colors <- scico(30, palette = 'berlin')
 
 mq_heatmap <- function(img, df, all_intcols, colSideColors, filter_to_sig, alpha, width, height, strip){
     # df is the output from either expand, stat, or filter