Mercurial > repos > lecorguille > xcms_summary
changeset 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 |
| files | abims_xcms_summary.xml lib.r repository_dependencies.xml xcms_summary.r |
| diffstat | 4 files changed, 27 insertions(+), 8 deletions(-) [+] |
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--- a/abims_xcms_summary.xml Tue May 12 16:39:28 2020 -0400 +++ b/abims_xcms_summary.xml Thu Sep 24 08:09:02 2020 +0000 @@ -1,4 +1,4 @@ -<tool id="abims_xcms_summary" name="xcms process history" version="@TOOL_VERSION@+galaxy1"> +<tool id="abims_xcms_summary" name="xcms process history" version="@TOOL_VERSION@+galaxy2"> <description>Create a summary of XCMS analysis</description> @@ -87,6 +87,10 @@ Changelog/News -------------- +**Version 3.6.1+galaxy2 - 23/09/2020** + +- BUGFIX: "Error: object 'sampleNamesList' not found" in case of .RData input from CAMERA + .. _News: https://bioconductor.org/packages/release/bioc/news/xcms/NEWS **Version 3.6.1+galaxy1 - 05/04/2020**
--- 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$sample_group], main=main, peakType = "none") legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1) }
--- a/repository_dependencies.xml Tue May 12 16:39:28 2020 -0400 +++ b/repository_dependencies.xml Thu Sep 24 08:09:02 2020 +0000 @@ -1,5 +1,5 @@ <?xml version="1.0" ?> <repositories> - <repository changeset_revision="544f6d2329ac" name="rdata_xcms_datatypes" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu"/> - <repository changeset_revision="4a51ab3d8ecf" name="rdata_camera_datatypes" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu"/> + <repository name="rdata_xcms_datatypes" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu" changeset_revision="544f6d2329ac"/> + <repository name="rdata_camera_datatypes" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu" changeset_revision="4a51ab3d8ecf"/> </repositories> \ No newline at end of file
--- a/xcms_summary.r Tue May 12 16:39:28 2020 -0400 +++ b/xcms_summary.r Thu Sep 24 08:09:02 2020 +0000 @@ -73,7 +73,10 @@ if (!exists("sampleNamesList")) sampleNamesList <- list("sampleNamesMakeNames"=make.names(sampnames(xobject))) } # if the RData come from CAMERA -if (exists("xa")) xobject <- xa@xcmsSet +if (exists("xa")) { + xobject <- xa@xcmsSet + if (!exists("sampleNamesList")) sampleNamesList <- list("sampleNamesMakeNames"=make.names(xa@xcmsSet@phenoData$sample_name)) +} # if the RData come from XCMS 3.x if (exists("xdata")) { xobject <- xdata