Mercurial > repos > lecorguille > xcms_group
changeset 12:e3eda5cff0b6 draft
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94
| author | lecorguille |
|---|---|
| date | Thu, 22 Dec 2016 05:59:36 -0500 |
| parents | dc29a74d307b |
| children | 206e5a968dc5 |
| files | lib.r macros.xml |
| diffstat | 2 files changed, 42 insertions(+), 3 deletions(-) [+] |
line wrap: on
line diff
--- a/lib.r Mon Nov 14 16:19:18 2016 -0500 +++ b/lib.r Thu Dec 22 05:59:36 2016 -0500 @@ -1,9 +1,12 @@ -# lib.r version="2.0.1" +# lib.r version="2.3" #Authors ABiMS TEAM #Lib.r for Galaxy Workflow4Metabo -#version 2.2 +#version 2.3 #Based on lib.r 2.1 #Modifications made by Guitton Yann +#2.3 Note +#correction for empty PDF when only 1 class +#2.2 Note #correct bug in Base Peak Chromatogram (BPC) option, not only TIC when scanrange used in xcmsSet #Note if scanrange is used a warning is prompted in R console but do not stop PDF generation @@ -114,7 +117,25 @@ legend("topright",paste(basename(files[c(classnames[[k]],classnames[[l]])])), col = colvect, lty = lty, pch = pch) }#end length ==2 + + #case where only one class + if (length(class)==1){ + k=1 + ylim = range(sapply(TIC, function(x) range(x[,2]))) + colvect<-NULL + plot(0, 0, type="n", xlim = xlim/60, ylim = ylim, main = paste("Base Peak Chromatograms \n","BPCs_",class[k], sep=""), xlab = "Retention Time (min)", ylab = "BPC") + for (j in 1:length(classnames[[k]])) { + tic <- TIC[[classnames[[k]][j]]] + # points(tic[,1]/60, tic[,2], col = cols[i], pch = pch[i], type="l") + points(tic[,1]/60, tic[,2], col = cols[classnames[[k]][j]], pch = pch[classnames[[k]][j]], type="l") + colvect<-append(colvect,cols[classnames[[k]][j]]) + } + + legend("topright",paste(basename(files[c(classnames[[k]])])), col = colvect, lty = lty, pch = pch) + + }#end length ==1 + dev.off() #pdf(pdfname,w=16,h=10) invisible(TIC) @@ -219,6 +240,25 @@ legend("topright",paste(basename(files[c(classnames[[k]],classnames[[l]])])), col = colvect, lty = lty, pch = pch) }#end length ==2 + + #case where only one class + if (length(class)==1){ + k=1 + ylim = range(sapply(TIC, function(x) range(x[,2]))) + + plot(0, 0, type="n", xlim = xlim/60, ylim = ylim, main = paste("Total Ion Chromatograms \n","TICs_",class[k], sep=""), xlab = "Retention Time (min)", ylab = "TIC") + colvect<-NULL + for (j in 1:length(classnames[[k]])) { + tic <- TIC[[classnames[[k]][j]]] + # points(tic[,1]/60, tic[,2], col = cols[i], pch = pch[i], type="l") + points(tic[,1]/60, tic[,2], col = cols[classnames[[k]][j]], pch = pch[classnames[[k]][j]], type="l") + colvect<-append(colvect,cols[classnames[[k]][j]]) + } + + legend("topright",paste(basename(files[c(classnames[[k]])])), col = colvect, lty = lty, pch = pch) + + }#end length ==1 + dev.off() #pdf(pdfname,w=16,h=10) invisible(TIC)
--- a/macros.xml Mon Nov 14 16:19:18 2016 -0500 +++ b/macros.xml Thu Dec 22 05:59:36 2016 -0500 @@ -2,7 +2,6 @@ <macros> <xml name="requirements"> <requirements> - <requirement type="package" version="3.1.2">R</requirement> <requirement type="package" version="0.4_1">r-snow</requirement> <requirement type="package" version="1.46.0">bioconductor-xcms</requirement> <requirement type="package" version="1.1_4">r-batch</requirement>