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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5763 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
corin 2011-05-04 20:10:47 +00:00
parent bcc688c1e9
commit b4654b0f47
1 changed files with 13 additions and 8 deletions
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21
R/DataProcessingReport/Tearsheet.R
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@ -32,16 +32,16 @@ for(squid in squids){
lane<-rbind(lane, addlanes) lane<-rbind(lane, addlanes)
samp<-rbind(samp, addsamps) samp<-rbind(samp, addsamps)
} }
print("Picard Data Obtained...")
gsa.read.gatkreport(paste(cmdargs$evalroot, ".eval", sep=""))->FCeval gsa.read.gatkreport(paste(cmdargs$evalroot, ".eval", sep=""))->FCeval
gsa.read.gatkreport(paste(cmdargs$evalroot, ".extraFC.eval", sep=""))->FCeval gsa.read.gatkreport(paste(cmdargs$evalroot, ".extraFC.eval", sep=""))->FCeval
gsa.read.gatkreport(paste(cmdargs$evalroot, ".extraFI.eval", sep=""))->FIeval
gsa.read.gatkreport(paste(cmdargs$evalroot, ".extraSA.eval", sep=""))->SAeval gsa.read.gatkreport(paste(cmdargs$evalroot, ".extraSA.eval", sep=""))->SAeval
print("Evals read")
tearsheet<-function(){ tearsheet<-function(){
pdf(file= cmdargs$tearout, width=22, height=17, pagecentre=TRUE, pointsize=24) pdf(file= cmdargs$tearout, width=22, height=17, pagecentre=TRUE, pointsize=24)
print("PDF created...")
#define layout #define layout
postable<-matrix(c(1, 1, 1, 1, rep(c(2, 2, 4, 4), 5), rep(c(3, 3, 4, 4), 3), rep(c(3,3,5,5), 5), 6,7,8,9), nrow=15, ncol=4, byrow=TRUE) postable<-matrix(c(1, 1, 1, 1, rep(c(2, 2, 4, 4), 5), rep(c(3, 3, 4, 4), 3), rep(c(3,3,5,5), 5), 6,7,8,9), nrow=15, ncol=4, byrow=TRUE)
layout(postable, heights=c(1, rep(.18, 13), 2), respect=FALSE) layout(postable, heights=c(1, rep(.18, 13), 2), respect=FALSE)
@ -49,11 +49,13 @@ tearsheet<-function(){
#prep for title bar #prep for title bar
drop<-read.jpeg(system.file("data", "tearsheetdrop.jpg", package="gsalib")) drop<-read.jpeg(system.file("data", "tearsheetdrop.jpg", package="gsalib"))
#plot title bar #plot title bar
par(mar=c(0,0,0,0)) par(mar=c(0,0,0,0))
plot(drop) plot(drop)
text(155, 50, cmdargs$title, family="serif", adj=c(0,0), cex=3, col=gray(.25)) text(155, 50, cmdargs$title, family="serif", adj=c(0,0), cex=3, col=gray(.25))
print("Title created...")
# Project summary # Project summary
projects = paste(squids, collapse=", "); projects = paste(squids, collapse=", ");
@ -73,7 +75,7 @@ tearsheet<-function(){
par(mar=c(0,0,1,0)) par(mar=c(0,0,1,0))
textplot(table1, col.rownames="darkblue", show.colnames=FALSE, cex=1.25, valign="top") textplot(table1, col.rownames="darkblue", show.colnames=FALSE, cex=1.25, valign="top")
title(main=sprintf("Project Summary (%s)\n", projects), family="sans", cex.main=1.25, line=-1) title(main=sprintf("Project Summary (%s)\n", projects), family="sans", cex.main=1.25, line=-1)
print("Project summary created...")
# Bases summary # Bases summary
reads_per_lane_mean = format(mean(lane$"PF Reads (HS)", na.rm=TRUE), 8, 3,1, scientific=TRUE); reads_per_lane_mean = format(mean(lane$"PF Reads (HS)", na.rm=TRUE), 8, 3,1, scientific=TRUE);
@ -138,6 +140,7 @@ tearsheet<-function(){
textplot(table2, rmar=1, col.rownames="dark blue", cex=1.25, valign="top") textplot(table2, rmar=1, col.rownames="dark blue", cex=1.25, valign="top")
title(main="Bases Summary", family="sans", cex.main=1.25, line=0) title(main="Bases Summary", family="sans", cex.main=1.25, line=0)
print("Bases summary created...")
# Sequencing summary # Sequencing summary
@ -186,7 +189,7 @@ tearsheet<-function(){
textplot(table3, rmar=1, col.rownames="dark blue", show.colnames=FALSE, cex=1.25, valign="top") textplot(table3, rmar=1, col.rownames="dark blue", show.colnames=FALSE, cex=1.25, valign="top")
title(main="Sequencing Summary", family="sans", cex.main=1.25, line=0) title(main="Sequencing Summary", family="sans", cex.main=1.25, line=0)
print("Sequencing summary created...")
# Variant summary # Variant summary
@ -205,7 +208,7 @@ tearsheet<-function(){
rownames(table4) = c("All", "Known", "Novel"); rownames(table4) = c("All", "Known", "Novel");
colnames(table4) = c("Found", "Ti/Tv ratio", "Expected Ti/Tv ratio"); colnames(table4) = c("Found", "Ti/Tv ratio", "Expected Ti/Tv ratio");
print("Variant summary created...")
par(mar=c(0,0,0,0)) par(mar=c(0,0,0,0))
textplot(table4, rmar=1, col.rownames="dark blue", cex=1.25, valign="top") textplot(table4, rmar=1, col.rownames="dark blue", cex=1.25, valign="top")
@ -255,8 +258,10 @@ tearsheet<-function(){
axis(1, at=c(1.5,5,8.5), lab=c("Missense", "Nonsense", "Silent"), cex=.5, tick=FALSE) axis(1, at=c(1.5,5,8.5), lab=c("Missense", "Nonsense", "Silent"), cex=.5, tick=FALSE)
legend("top", c("All", "Known", "Novel"), fill=c("dark gray", "blue", "red"), cex=.7); legend("top", c("All", "Known", "Novel"), fill=c("dark gray", "blue", "red"), cex=.7);
print("Graphs created...")
dev.off() dev.off()
print("All done!")
} }
tearsheet() tearsheet()