diff --git a/R/DataProcessingReport/Tearsheet.R b/R/DataProcessingReport/Tearsheet.R index 6104b6419..127c48250 100644 --- a/R/DataProcessingReport/Tearsheet.R +++ b/R/DataProcessingReport/Tearsheet.R @@ -32,16 +32,16 @@ for(squid in squids){ lane<-rbind(lane, addlanes) samp<-rbind(samp, addsamps) } - +print("Picard Data Obtained...") gsa.read.gatkreport(paste(cmdargs$evalroot, ".eval", sep=""))->FCeval gsa.read.gatkreport(paste(cmdargs$evalroot, ".extraFC.eval", sep=""))->FCeval -gsa.read.gatkreport(paste(cmdargs$evalroot, ".extraFI.eval", sep=""))->FIeval gsa.read.gatkreport(paste(cmdargs$evalroot, ".extraSA.eval", sep=""))->SAeval - +print("Evals read") tearsheet<-function(){ pdf(file= cmdargs$tearout, width=22, height=17, pagecentre=TRUE, pointsize=24) - + print("PDF created...") + #define layout postable<-matrix(c(1, 1, 1, 1, rep(c(2, 2, 4, 4), 5), rep(c(3, 3, 4, 4), 3), rep(c(3,3,5,5), 5), 6,7,8,9), nrow=15, ncol=4, byrow=TRUE) layout(postable, heights=c(1, rep(.18, 13), 2), respect=FALSE) @@ -49,11 +49,13 @@ tearsheet<-function(){ #prep for title bar drop<-read.jpeg(system.file("data", "tearsheetdrop.jpg", package="gsalib")) + #plot title bar par(mar=c(0,0,0,0)) plot(drop) text(155, 50, cmdargs$title, family="serif", adj=c(0,0), cex=3, col=gray(.25)) - + print("Title created...") + # Project summary projects = paste(squids, collapse=", "); @@ -73,7 +75,7 @@ tearsheet<-function(){ par(mar=c(0,0,1,0)) 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) - + print("Project summary created...") # Bases summary 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") title(main="Bases Summary", family="sans", cex.main=1.25, line=0) + print("Bases summary created...") # Sequencing summary @@ -186,7 +189,7 @@ tearsheet<-function(){ 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) - + print("Sequencing summary created...") # Variant summary @@ -205,7 +208,7 @@ tearsheet<-function(){ rownames(table4) = c("All", "Known", "Novel"); colnames(table4) = c("Found", "Ti/Tv ratio", "Expected Ti/Tv ratio"); - + print("Variant summary created...") par(mar=c(0,0,0,0)) 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) legend("top", c("All", "Known", "Novel"), fill=c("dark gray", "blue", "red"), cex=.7); + print("Graphs created...") dev.off() + print("All done!") } tearsheet() \ No newline at end of file