# HG changeset patch # User workflow4metabolomics # Date 1595337390 0 # Node ID 6f3567245d0c0f002f20bcea5d26fda7b0a10293 # Parent 053e81c58b115a62671ab19215fb280a09a8f03c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 0dcc8bcb1e645574c7f81ec1a43f86be38acd065" diff -r 053e81c58b11 -r 6f3567245d0c abims_xcms_group.xml --- a/abims_xcms_group.xml Tue Apr 28 13:33:39 2020 +0000 +++ b/abims_xcms_group.xml Tue Jul 21 13:16:30 2020 +0000 @@ -1,4 +1,4 @@ - + Perform the correspondence, the grouping of chromatographic peaks within and between samples. diff -r 053e81c58b11 -r 6f3567245d0c lib.r --- a/lib.r Tue Apr 28 13:33:39 2020 +0000 +++ b/lib.r Tue Jul 21 13:16:30 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]) @@ -241,7 +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")