| Previous changeset 25:a066b8581b97 (2020-04-28) Next changeset 27:d45a786cbc40 (2021-04-07) |
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Commit message:
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 0dcc8bcb1e645574c7f81ec1a43f86be38acd065" |
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modified:
abims_xcms_group.xml lib.r |
| b |
| diff -r a066b8581b97 -r 0d05d0458376 abims_xcms_group.xml --- a/abims_xcms_group.xml Tue Apr 28 09:34:27 2020 -0400 +++ b/abims_xcms_group.xml Tue Jul 21 09:17:27 2020 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="abims_xcms_group" name="xcms groupChromPeaks (group)" version="@TOOL_VERSION@+galaxy1"> +<tool id="abims_xcms_group" name="xcms groupChromPeaks (group)" version="@TOOL_VERSION@+galaxy2"> <description>Perform the correspondence, the grouping of chromatographic peaks within and between samples.</description> |
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| diff -r a066b8581b97 -r 0d05d0458376 lib.r --- a/lib.r Tue Apr 28 09:34:27 2020 -0400 +++ b/lib.r Tue Jul 21 09:17:27 2020 -0400 |
| [ |
| @@ -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") |