Mercurial > repos > artbio > probecoverage
changeset 1:ebe5ec2e244d draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/probecoverage commit 0d963d33685a407873cd17924c7ec2b6255b006f
| author | artbio |
|---|---|
| date | Sat, 23 Sep 2017 12:56:17 -0400 |
| parents | dbeb4a0abfc6 |
| children | 35d2db3753d9 |
| files | probecoverage.r probecoverage.xml test-data/graph.pdf |
| diffstat | 3 files changed, 7 insertions(+), 3 deletions(-) [+] |
line wrap: on
line diff
--- a/probecoverage.r Sat Sep 23 05:11:49 2017 -0400 +++ b/probecoverage.r Sat Sep 23 12:56:17 2017 -0400 @@ -32,6 +32,7 @@ ## function cumul <- function(x,y) sum(Table[,y]/(Table$end-Table$start) > x)/length(Table$chromosome) +scaleFUN <- function(x) sprintf("%.3f", x) ## end of function ## let's do a dataframe before plotting @@ -50,12 +51,15 @@ ## GRAPHS pdf(file=args$output) -ggplot(data=graphpoints, aes(x=Depth, y=sample_value, group=Samples, colour=Samples)) + +ggplot(data=graphpoints, aes(x=Depth, y=sample_value, colour=Samples)) + geom_line(size=1) + scale_x_continuous(trans='log2', breaks = 2^(seq(0,log(maxdepth, 2)))) + - scale_y_continuous(breaks = seq(0, maxfrac, by=maxfrac/10)) + + scale_y_continuous(breaks = seq(0, maxfrac, by=maxfrac/10), labels=scaleFUN) + labs(x=args$xlab, y=args$ylab, title=args$title) + theme(legend.position="top", legend.title=element_blank(), legend.text=element_text(colour="blue", size=7)) + + +## facet_wrap(~Samples, ncol=2) devname=dev.off()
--- a/probecoverage.xml Sat Sep 23 05:11:49 2017 -0400 +++ b/probecoverage.xml Sat Sep 23 12:56:17 2017 -0400 @@ -1,4 +1,4 @@ -<tool id="probecoverage" name="Probe Coverage" version="0.1.0"> +<tool id="probecoverage" name="Probe Coverage" version="0.2.0"> <description></description> <requirements> <requirement type="package" version="1.4.1">samtools</requirement>