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Minor formatting udpates to deal with long bait names, multiple sequencer types, and date formatting 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5072 348d0f76-0448-11de-a6fe-93d51630548a
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corin 2011-01-25 19:02:40 +00:00
parent 17ba75e502
commit b22f82d5dd
1 changed files with 31 additions and 17 deletions
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48
R/DataProcessingReport/GetTearsheetStats.R
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@ -79,13 +79,12 @@ tearsheet<-function(){
#prep for title bar
full<-strsplit(cmdargs$evalroot, "/")
name<-strsplit(full[[1]][length(full[[1]])], ".",fixed=TRUE)[[1]][1]
title=paste(name, ": TEAR SHEET", sep="")
drop<-read.jpeg(system.file(tearsheetdrop, package="gsalib"))
#plot title bar
par(mar=c(0,0,0,0))
plot(drop)
text(110, 45, title, family="serif", adj=c(0,0), cex=3, col=gray(.25))
text(110, 45, name, family="serif", adj=c(0,0), cex=3, col=gray(.25))
# Project summary
@ -97,7 +96,15 @@ tearsheet<-function(){
sequencing_protocol = "Hybrid selection"; #can this be extracted?
bait_design = paste(unique(dproj$"Bait Set"), collapse=", ");
bait_design = paste(dimnames(table(dproj$"Bait Set"))[[1]][order(table(dproj$"Bait Set"), decreasing=TRUE)], collapse=", ");
if(nchar(bait_design)>50){
bait_design<-strsplit(bait_design, ", ")[[1]][1]
}
if(nchar(bait_design)>50){
bait_design<-strsplit(bait_design, ".Homo")[[1]][1]
}
callable_target = paste(unique(dproj$"Target Territory"), collapse=", ");
@ -179,6 +186,10 @@ tearsheet<-function(){
instrument <- c(instrument, "Illumina HiSeq")
}
if(length(instrument)>1){
instrument<-paste(instrument[1], instrument[2], sep=" and ")
}
used_lanes = nrow(dproj);
unused_lanes_by_sequencing = 0; #can we get this?
unused_lanes_by_analysis = 0;
@ -196,28 +207,31 @@ tearsheet<-function(){
read_length_median = median(dproj$"Mean Read Length (P)");
date = dproj$"Run Date";
date = sub("JAN", "01", date);
date = sub("FEB", "02", date);
date = sub("MAR", "03", date);
date = sub("APR", "04", date);
date = sub("MAY", "05", date);
date = sub("JUN", "06", date);
date = sub("JUL", "07", date);
date = sub("AUG", "08", date);
date = sub("SEP", "09", date);
date = sub("OCT", "10", date);
date = sub("NOV", "11", date);
date = sub("DEC", "12", date);
# date = sub("JAN", "01", date);
# date = sub("FEB", "02", date);
# date = sub("MAR", "03", date);
# date = sub("APR", "04", date);
# date = sub("MAY", "05", date);
# date = sub("JUN", "06", date);
# date = sub("JUL", "07", date);
# date = sub("AUG", "08", date);
# date = sub("SEP", "09", date);
# date = sub("OCT", "10", date);
# date = sub("NOV", "11", date);
# date = sub("DEC", "12", date);
date = date[order(as.Date(date, format="%d-%m-%Y"))];
start_date = date[1];
end_date = date[length(date)];
table3<-rbind(paste(instrument), used_lanes, sprintf("%s rejected by sequencing, %s by analysis\n", unused_lanes_by_sequencing, unused_lanes_by_analysis), sprintf("%0.1f +/- %0.1f lanes (median=%0.1f)\n", lanes_per_sample_mean, lanes_per_sample_sd, lanes_per_sample_median), sprintf("%s paired, %s widowed, %s single\n", lanes_paired, lanes_widowed, lanes_single), sprintf("%0.1f +/- %0.1f bases (median=%0.1f)\n", read_length_mean, read_length_sd, read_length_median), sprintf("\tSequencing dates: %s to %s\n", start_date, end_date))
print(nrow(table3))
print(ncol(table3))
print(used_lanes)
print(instrument)
rownames(table3)<-c("Sequencer", "Used lanes", "Unused lanes","Used lanes/sample", "Lane pariteies", "Read legnths", "Sequencing dates")
rownames(table3)<-c("Sequencer", "Used lanes", "Unused lanes","Used lanes/sample", "Lane parities", "Read lengths", "Sequencing dates")
par(mar=c(4,4,4,4))
textplot(table3, rmar=1, col.rownames="dark blue", show.colnames=FALSE, cex=1.25)
title(main="Sequencing Summary", family="sans", cex.main=1.75)