Mercurial > repos > lecorguille > xcms_summary
diff lib.r @ 27:bed23aa27b4b draft
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 50478425b4773ebcb393c0e31f1e622b7406dcbb"
author | workflow4metabolomics |
---|---|
date | Thu, 24 Sep 2020 08:09:02 +0000 |
parents | db6549f27ad1 |
children | 018a9771de28 |
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--- a/lib.r Tue May 12 16:39:28 2020 -0400 +++ b/lib.r Thu Sep 24 08:09:02 2020 +0000 @@ -149,7 +149,11 @@ 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]} @@ -172,7 +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]) @@ -241,10 +249,14 @@ 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") + plot(chrom, col = group_colors[chrom$sample_group], main=main, peakType = "none") legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1) }