diff --git a/tools/rgenetics/rgGRR.py b/tools/rgenetics/rgGRR.py index 75c59ed3553..07da056b375 100644 --- a/tools/rgenetics/rgGRR.py +++ b/tools/rgenetics/rgGRR.py @@ -78,7 +78,7 @@ class NullDevice: pass tempstderr = sys.stderr # save -sys.stderr = NullDevice() +#sys.stderr = NullDevice() # need to avoid blather about deprecation and other strange stuff from scipy # the current galaxy job runner assumes that # the job is in error if anything appears on sys.stderr diff --git a/tools/rgenetics/rgManQQ.py b/tools/rgenetics/rgManQQ.py index 11715de05c1..6c8fe182b50 100644 --- a/tools/rgenetics/rgManQQ.py +++ b/tools/rgenetics/rgManQQ.py @@ -75,25 +75,25 @@ manhattan = function(chrom=NULL,offset=NULL,pvals=NULL, title=NULL, max.y="max", # only makes sense if genome wide is assumed - we could have a fine mapping region? if (annotate) d.annotate=d[as.numeric(substr(d$SNP,3,100)) %in% SNPlist, ] - plot=qplot(pos,logp,data=d, ylab=expression(-log[10](italic(p))) , colour=factor(CHR)) - plot=plot+scale_x_continuous(name="Chromosome", breaks=ticks, labels=(unique(d$CHR))) - plot=plot+scale_y_continuous(limits=c(0,maxy), breaks=1:maxy, labels=1:maxy) - plot=plot+scale_colour_manual(value=mycols) - if (annotate) plot=plot + geom_point(data=d.annotate, colour=I("green3")) - plot=plot + opts(legend.position = "none") - plot=plot + opts(title=title) - plot=plot+opts( + manplot=qplot(pos,logp,data=d, ylab=expression(-log[10](italic(p))) , colour=factor(CHR)) + manplot=manplot+scale_x_continuous(name="Chromosome", breaks=ticks, labels=(unique(d$CHR))) + manplot=manplot+scale_y_continuous(limits=c(0,maxy), breaks=1:maxy, labels=1:maxy) + manplot=manplot+scale_colour_manual(value=mycols) + if (annotate) { manplot=manplot + geom_point(data=d.annotate, colour=I("green3")) } + manplot=manplot + opts(legend.position = "none") + manplot=manplot + opts(title=title) + manplot=manplot+opts( panel.background=theme_blank(), axis.text.x=theme_text(size=size.x.labels, colour="grey50"), axis.text.y=theme_text(size=size.y.labels, colour="grey50"), axis.ticks=theme_segment(colour=NA) ) - #plot = plot + opts(panel.grid.y.minor=theme_blank(),panel.grid.y.major=theme_blank()) - #plot = plot + opts(panel.grid.major=theme_blank()) + #manplot = manplot + opts(panel.grid.y.minor=theme_blank(),panel.grid.y.major=theme_blank()) + #manplot = manplot + opts(panel.grid.major=theme_blank()) - if (suggestiveline) plot=plot+geom_hline(yintercept=suggestiveline,colour="blue", alpha=I(1/3)) - if (genomewideline) plot=plot+geom_hline(yintercept=genomewideline,colour="red") - plot + if (suggestiveline) manplot=manplot+geom_hline(yintercept=suggestiveline,colour="blue", alpha=I(1/3)) + if (genomewideline) manplot=manplot+geom_hline(yintercept=genomewideline,colour="red") + manplot } else { stop("Make sure your data frame contains columns CHR, BP, and P") } @@ -110,12 +110,12 @@ qq = function(pvector, title=NULL, spartan=F) { # ylab=expression(Observed~~-log[10](italic(p))), xlim=c(0,max(e)), ylim=c(0,max(e))) # lines(e,e,col="red") #You'll need ggplot2 installed to do the rest - plot=qplot(e,o, xlim=c(0,max(e)), ylim=c(0,max(o))) + stat_abline(intercept=0,slope=1, col="red") - plot=plot+opts(title=title) - plot=plot+scale_x_continuous(name=expression(Expected~~-log[10](italic(p)))) - plot=plot+scale_y_continuous(name=expression(Observed~~-log[10](italic(p)))) + qq=qplot(e,o, xlim=c(0,max(e)), ylim=c(0,max(o))) + stat_abline(intercept=0,slope=1, col="red") + qq=qq+opts(title=title) + qq=qq+scale_x_continuous(name=expression(Expected~~-log[10](italic(p)))) + qq=qq+scale_y_continuous(name=expression(Observed~~-log[10](italic(p)))) if (spartan) plot=plot+opts(panel.background=theme_rect(col="grey50"), panel.grid.minor=theme_blank()) - plot + qq } """ @@ -140,6 +140,7 @@ if (plen > 0) { mytitle = paste('p=',cname,', ',title,sep='') myfname = chartr(' ','_',cname) myqqplot = qq(rawd[,pvalscolumn],title=mytitle) + ggsave(filename=paste(myfname,"qqplot.png",sep='_'),myqqplot,width=8,height=11) print(paste('## qqplot on',cname,'done')) if ((chromcolumn > 0) & (offsetcolumn > 0)) { if (doreorder) { @@ -151,13 +152,12 @@ if (plen > 0) { print(paste('## manhattan on',cname,'starting',chromcolumn,offsetcolumn,pvalscolumn)) mymanplot= manhattan(chrom=rawd[,chromcolumn],offset=rawd[,offsetcolumn],pvals=rawd[,pvalscolumn],title=mytitle,grey=grey) print(paste('## manhattan plot on',cname,'done')) - ggsave(file=paste(myfname,"manhattan.png",sep='_'),mymanplot,width=11,height=8,dpi=100) + ggsave(filename=paste(myfname,"manhattan.png",sep='_'),mymanplot,width=11,height=8) } else { print(paste('chrom column =',chromcolumn,'offset column = ',offsetcolumn, 'so no Manhattan plot - supply both chromosome and offset as numerics for Manhattan plots if required')) } - ggsave(file=paste(myfname,"qqplot.png",sep='_'),myqqplot,width=8,height=11,dpi=100) } else { print(paste('pvalue column =',pvalscolumn,'Cannot parse it so no plots possible')) @@ -177,9 +177,10 @@ def doManQQ(input_fname,chrom_col,offset_col,pval_cols,title,grey,ctitle,outdir) to make them do our bidding - and save the resulting code for posterity this can be called externally, I guess...for QC eg? """ - rcmd = '%s%s' % (rcode,rcode2 % (input_fname,chrom_col,offset_col,pval_cols,title,grey)) rlog,flist = RRun(rcmd=rcmd,title=ctitle,outdir=outdir) + rlog.append('## R script=') + rlog.append(rcmd) return rlog,flist diff --git a/tools/rgenetics/rgManQQ.xml b/tools/rgenetics/rgManQQ.xml index e307f4e822e..228c3c567b4 100644 --- a/tools/rgenetics/rgManQQ.xml +++ b/tools/rgenetics/rgManQQ.xml @@ -42,14 +42,10 @@ - - - - + - diff --git a/tools/rgenetics/rgtest.sh b/tools/rgenetics/rgtest.sh index 07810153969..884b2bba4ff 100755 --- a/tools/rgenetics/rgtest.sh +++ b/tools/rgenetics/rgtest.sh @@ -41,7 +41,7 @@ CL="python $TOOLPATH/$TOOL.py "$INPATH/smallwgaP.xls" $NPRE ${OUTPATH}/${NPRE}.h #python /opt/galaxy/tools/rgenetics/rgManQQ.py /opt/galaxy/test-data/smallwgaP.xls rgManQQtest1 #/opt/galaxy/test-data/rgtestouts/rgManQQ/rgManQQtest1.html /opt/galaxy/test-data/rgtestouts/rgManQQ 1 2 5,7 echo "Testing $TOOL using $CL" -python $TOOLPATH/$TOOL.py "$INPATH/smallwgaP.xls" $NPRE ${OUTPATH}/${NPRE}.html $OUTPATH 1 2 5,7 0 +python $TOOLPATH/$TOOL.py "$INPATH/smallwgaP.xls" $NPRE ${OUTPATH}/${NPRE}.html $OUTPATH 1 2 7 0 TOOL="rgfakePhe" NPRE=${TOOL}test1 OUTPATH="$OROOT/$TOOL" diff --git a/tools/rgenetics/rgutils.py b/tools/rgenetics/rgutils.py index fb95275ed20..0538d71f93b 100644 --- a/tools/rgenetics/rgutils.py +++ b/tools/rgenetics/rgutils.py @@ -122,32 +122,36 @@ def RRun(rcmd=[],outdir=None,title='myR',tidy=True): tempout=False rname = '%s.R' % title stoname = '%s.R.log' % title + cwd = os.getcwd() if outdir: # want a specific path try: os.makedirs(outdir) # might not be there yet... except: pass - else: - tempout = True - outdir = tempfile.mkdtemp(prefix=title) + os.chdir(outdir) if type(rcmd) == type([]): script = '\n'.join(rcmd) else: # string script = rcmd sto = file(stoname,'w') - rscriptname = os.path.join(outdir,rname) - rscript = file(rscriptname,'w') + rscript = file(rname,'w') rscript.write(script) rscript.write('\n#R script autogenerated by rgenetics/rgutils.py on %s\n' % timenow()) rscript.close() - vcl = '%s --slave --vanilla < %s' % (rexe,rscriptname) - x = subprocess.Popen(vcl,shell=True,stderr=sto,stdout=sto,cwd=outdir) + vcl = '%s --slave --vanilla < %s' % (rexe,rname) + if outdir: + x = subprocess.Popen(vcl,shell=True,stderr=sto,stdout=sto,cwd=outdir) + else: + x = subprocess.Popen(vcl,shell=True,stderr=sto,stdout=sto) retval = x.wait() sto.close() rlog = file(stoname,'r').readlines() if retval <> 0: rlog.insert(0,'Nonzero exit code = %d' % retval) # indicate failure - flist = os.listdir(outdir) + if outdir: + flist = os.listdir(outdir) + else: + flist = os.listdir(os.getcwd()) flist.sort flist = [(x,x) for x in flist] for i,x in enumerate(flist): @@ -155,16 +159,8 @@ def RRun(rcmd=[],outdir=None,title='myR',tidy=True): flist[i] = (x,'R script for %s' % title) elif x == stoname: flist[i] = (x,'R log for %s' % title) - if tidy and tempout: # we used a temp one - fix that - flist = os.listdir(outdir) - for f in flist: - if os.path.isdir(f): - flist2 = os.listdir(f) - for f2 in flist2: - os.unlink(os.path.abspath(f2)) - else: - os.unlink(os.path.abspath(f)) - os.rmdir(outdir) + if outdir: + os.chdir(cwd) return rlog,flist # for html layout def runPlink(bfn='bar',ofn='foo',logf=None,plinktasks=[],cd='./',vclbase = []):