Mercurial > repos > sblanck > smagexp
changeset 28:49ce6fbe11de draft
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit cb90fdea2a64908e301355aef89de403e107764d
| author | sblanck |
|---|---|
| date | Thu, 21 Jun 2018 04:28:19 -0400 |
| parents | 75612b9d44cf |
| children | 102e4ef8fed2 |
| files | MetaRNASeq.R MetaRNASeq_tpl.html MetaRNAseq.xml |
| diffstat | 3 files changed, 30 insertions(+), 9 deletions(-) [+] |
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--- a/MetaRNASeq.R Thu Mar 22 10:48:15 2018 -0400 +++ b/MetaRNASeq.R Thu Jun 21 04:28:19 2018 -0400 @@ -153,8 +153,13 @@ # combinations library(metaRNASeq) +library(UpSetR) fishcomb<-fishercomb(rawpval, BHth=alpha) warning(length(rawpval)) + +#nrep=c(length(listFiles)) + + invnormcomb<-invnorm(rawpval, nrep=c(8,8), BHth=alpha) #DE[["fishercomb"]]<-ifelse(fishcomb$adjpval<=alpha,1,0) #DE[["invnormcomb"]]<-ifelse(invnormcomb$adjpval<=alpha,1,0) @@ -185,12 +190,25 @@ #write DE outputfile write.table(conflits, outputfile,sep="\t",,row.names=FALSE) library(VennDiagram) -DE_num=apply(DEresults, 2, FUN=function(x) which(x==1)) -venn.plot<-venn.diagram(x=as.list(DE_num),filename=NULL, col="black", fill=1:length(DE_num)+1,alpha=0.6) -temp.venn.plot = file.path( html.files.path, paste("venn.png")) -png(temp.venn.plot,width=500,height=500) -grid.draw(venn.plot) -dev.off() +DE_num=apply(keepDE[,1:(length(listfiles)+2)], 2, FUN=function(x) which(x==1)) +#DE_num=apply(DEresults, 2, FUN=function(x) which(x==1)) +if (length(listfiles<=2)) { + title="VENN DIAGRAM" + width=500 + venn.plot<-venn.diagram(x=as.list(DE_num),filename=NULL, col="black", fill=1:length(DE_num)+1,alpha=0.6) + temp.venn.plot = file.path( html.files.path, paste("venn.png")) + png(temp.venn.plot,width=width,height=500) + grid.draw(venn.plot) + dev.off() +} else { + title="UPSETR DIAGRAM" + width=1000 + png(temp.venn.plot,width=width,height=500) + upset(fromList(as.list(DE_num)), order.by = "freq") + dev.off() + +} + library(jsonlite) matrixConflits=as.matrix(conflits) @@ -210,6 +228,8 @@ htmlfile=gsub(x=htmlfile,pattern = "###FISHSUMMARYJSON###",replacement = summaryFishcombjson, fixed = TRUE) htmlfile=gsub(x=htmlfile,pattern = "###INVSUMMARYJSON###",replacement = summaryinvnormjson, fixed = TRUE) htmlfile=gsub(x=htmlfile,pattern = "###VENN###",replacement = vennFilename, fixed = TRUE) +htmlfile=gsub(x=htmlfile,pattern = "###WIDTH##",replacement = as.character(width), fixed = TRUE) +htmlfile=gsub(x=htmlfile,pattern = "###TITLE##",replacement = as.character(width), fixed = TRUE) write(htmlfile,result.html) #library(VennDiagram)
--- a/MetaRNASeq_tpl.html Thu Mar 22 10:48:15 2018 -0400 +++ b/MetaRNASeq_tpl.html Thu Jun 21 04:28:19 2018 -0400 @@ -139,8 +139,8 @@ <body> <table><tr><td> -<h2>Venn diagram</h2> -<img src='###VENN###' height="400" width="400"><br/> +<h2>###TITLE##</h2> +<img src='###VENN###' height="500" width=###WIDTH##><br/> </td><td> </td></tr></table>
--- a/MetaRNAseq.xml Thu Mar 22 10:48:15 2018 -0400 +++ b/MetaRNAseq.xml Thu Jun 21 04:28:19 2018 -0400 @@ -1,4 +1,4 @@ -<tool id="metarnaseq" name="RNA-seq data meta-analysis" version="1.0.0"> +<tool id="metarnaseq" name="RNA-seq data meta-analysis" version="1.1.0"> <description>Performs meta-analysis thanks to metaRNAseq</description> @@ -10,6 +10,7 @@ <requirement type="package">r-jsonlite</requirement> <requirement type="package">r-metarnaseq</requirement> <requirement type="package">r-optparse</requirement> + <requirement type="package" version="1.3.3">r-upsetr</requirement> </requirements> <stdio>