Mercurial > repos > davidvanzessen > mutation_analysis
changeset 105:e4957ad476a2 draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Thu, 23 Jun 2016 03:58:03 -0400 |
| parents | 603a10976e9c |
| children | 074ae1e30e8f |
| files | aa_histogram.r tmp/igat.r wrapper.sh |
| diffstat | 3 files changed, 20 insertions(+), 22 deletions(-) [+] |
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--- a/aa_histogram.r Wed Jun 22 10:07:28 2016 -0400 +++ b/aa_histogram.r Thu Jun 23 03:58:03 2016 -0400 @@ -20,20 +20,8 @@ dat_freq = mutations.at.position / aa.at.position dat_dt = data.frame(i=1:length(dat_freq), freq=dat_freq) -print("---------------- weird stuff ----------------") - -options(width=220) - -print(dat[,20:40]) - -print(dat_dt) #need this or it will fail???? - print("---------------- plot ----------------") -#also need these two, I don't even know... -print(paste("dat_freq", length(dat_freq))) -print(paste("dat_dt", nrow(dat_dt))) - m = ggplot(dat_dt, aes(x=i, y=freq)) + theme(axis.text.x = element_text(angle = 90, hjust = 1)) m = m + geom_bar(stat="identity", colour = "black", fill = "darkgrey", alpha=0.8) + scale_x_continuous(breaks=1:length(dat_freq), labels=1:length(dat_freq)) m = m + annotate("segment", x = 0.5, y = -0.05, xend=26.5, yend=-0.05, colour="darkgreen", size=1) + annotate("text", x = 13, y = -0.1, label="FR1") @@ -45,9 +33,7 @@ print("---------------- write/print ----------------") -print("writing dat_dt") #need this write.table(dat_dt, paste(dirname(outfile), "/aa_histogram_", gene, ".txt", sep=""), sep="\t",quote=F,row.names=F,col.names=T) -print("writing png") #also need this, file is haunted png(filename=outfile, width=1280, height=720) print(m) dev.off()
--- a/tmp/igat.r Wed Jun 22 10:07:28 2016 -0400 +++ b/tmp/igat.r Thu Jun 23 03:58:03 2016 -0400 @@ -13,14 +13,14 @@ merged = merged[!grepl("unmatched", merged$best_match),] for(f in list.files(imgt.dir, pattern="*.txt$")){ - print(paste("filtering", f)) + #print(paste("filtering", f)) path = paste(imgt.dir, f, sep="") dat = read.table(path, header=T, sep="\t", fill=T, quote="", stringsAsFactors=F) dat = dat[dat$Sequence.ID %in% merged$Sequence.ID,] - if(nrow(dat) > 0 & "FR1.IMGT" %in% colnames(dat)){ - dat$FR1.IMGT = "" + if(nrow(dat) > 0 & grepl("^8_", f)){ #change the FR1 columns to 0 in the "8_..." file + dat[,grepl("^FR1", names(dat))] = 0 } write.table(dat, path, quote=F, sep="\t", row.names=F, col.names=T)
--- a/wrapper.sh Wed Jun 22 10:07:28 2016 -0400 +++ b/wrapper.sh Thu Jun 23 03:58:03 2016 -0400 @@ -146,11 +146,23 @@ python $dir/mutation_analysis.py --input $outdir/merged.txt --genes $classes --includefr1 "${include_fr1}" --output $outdir/hotspot_analysis.txt echo "---------------- aa_histogram.r ----------------" -echo "---------------- aa_histogram.r ----------------<br />" >> $output +echo "---------------- aa_histogram.r ----------------<br />" >> $log Rscript $dir/aa_histogram.r $outdir/aa_mutations.txt $outdir/aa_histogram.png "" 2>&1 + +echo "---------------- aa_histogram.r ca ----------------" +echo "---------------- aa_histogram.r ca ----------------<br />" >> $log + Rscript $dir/aa_histogram.r $outdir/aa_mutations_ca.txt $outdir/aa_histogram_ca.png "ca" 2>&1 + +echo "---------------- aa_histogram.r cg ----------------" +echo "---------------- aa_histogram.r cg ----------------<br />" >> $log + Rscript $dir/aa_histogram.r $outdir/aa_mutations_cg.txt $outdir/aa_histogram_cg.png "cg" 2>&1 + +echo "---------------- aa_histogram.r cm ----------------" +echo "---------------- aa_histogram.r cm ----------------<br />" >> $log + Rscript $dir/aa_histogram.r $outdir/aa_mutations_cm.txt $outdir/aa_histogram_cm.png "cm" 2>&1 genes=(ca ca1 ca2 cg cg1 cg2 cg3 cg4 cm) @@ -367,10 +379,10 @@ echo "</table>" >> $outdir/base_overview.html +mv $log $outdir/log.html + +cp $outdir/index.html $log + echo "---------------- Done! ----------------" echo "---------------- Done! ----------------<br />" >> $log -mv $log $outdir/log.html - -mv $outdir/index.html $log -