diff lib.r @ 24:c8011370e90f draft

"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 0dcc8bcb1e645574c7f81ec1a43f86be38acd065"

--- a/lib.r	Thu Feb 13 06:43:08 2020 -0500
+++ b/lib.r	Wed Jul 29 05:10:58 2020 -0400
@@ -149,14 +149,20 @@
 
     par(mfrow = c(3, 1), mar = c(4, 4, 1, 0.5))
 
-    group_colors <- brewer.pal(length(unique(xdata$sample_group)), "Set1")
+    if(length(unique(xdata$sample_group))<10){
+        group_colors <- brewer.pal(length(unique(xdata$sample_group)), "Set1")
+    }else{
+        group_colors <- hcl.colors(length(unique(xdata$sample_group)), palette="Dark 3")
+    }
     names(group_colors) <- unique(xdata$sample_group)
+    col_per_samp <- as.character(xdata$sample_group)
+    for(i in 1:length(group_colors)){col_per_samp[col_per_samp==(names(group_colors)[i])]<-group_colors[i]}
 
     xlim <- c(min(featureDefinitions(xdata)$rtmin), max(featureDefinitions(xdata)$rtmax))
     for (i in 1:nrow(featureDefinitions(xdata))) {
         mzmin = featureDefinitions(xdata)[i,]$mzmin
         mzmax = featureDefinitions(xdata)[i,]$mzmax
-        plotChromPeakDensity(xdata, param = param, mz=c(mzmin,mzmax), col=group_colors, pch=16, xlim=xlim, main=paste(round(mzmin,mzdigit),round(mzmax,mzdigit)))
+        plotChromPeakDensity(xdata, param = param, mz=c(mzmin,mzmax), col=col_per_samp, pch=16, xlim=xlim, main=paste(round(mzmin,mzdigit),round(mzmax,mzdigit)))
         legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1)
     }
 
@@ -170,7 +176,11 @@
     pdf(file="raw_vs_adjusted_rt.pdf", width=16, height=12)
 
     # Color by group
-    group_colors <- brewer.pal(length(unique(xdata$sample_group)), "Set1")
+    if(length(unique(xdata$sample_group))<10){
+        group_colors <- brewer.pal(length(unique(xdata$sample_group)), "Set1")
+    }else{
+        group_colors <- hcl.colors(length(unique(xdata$sample_group)), palette="Dark 3")
+    }
     if (length(group_colors) > 1) {
         names(group_colors) <- unique(xdata$sample_group)
         plotAdjustedRtime(xdata, col = group_colors[xdata$sample_group])
@@ -239,7 +249,11 @@
     pdf(pdfname, width=16, height=10)
 
     # Color by group
-    group_colors <- brewer.pal(length(unique(xdata$sample_group)), "Set1")
+    if(length(unique(xdata$sample_group))<10){
+        group_colors <- brewer.pal(length(unique(xdata$sample_group)), "Set1")
+    }else{
+        group_colors <- hcl.colors(length(unique(xdata$sample_group)), palette="Dark 3")
+    }
     if (length(group_colors) > 1) {
         names(group_colors) <- unique(xdata$sample_group)
         plot(chrom, col = group_colors[as.factor(chrom$sample_group)], main=main, peakType = "none")