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Some minor tweaks to the tearsheet generator that incorperate the gsalib more universally and create a more accurate output 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5021 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
corin 2011-01-19 20:27:02 +00:00
parent c901fb6d70
commit dfcd45181a
1 changed files with 14 additions and 11 deletions
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25
R/DataProcessingReport/GetTearsheetStats.R
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@ -6,10 +6,7 @@
##change layouts so that it looks better ##change layouts so that it looks better
##get sample numbers in correctly ##get sample numbers in correctly
.libPaths('/humgen/gsa-firehose2/pipeline/repositories/StingProduction/R/')
.libPaths('~/Sting/R/') #but make sure this is universal
#put use scripts here
suppressMessages(library(gplots)); suppressMessages(library(gplots));
suppressMessages(library(ReadImages)); suppressMessages(library(ReadImages));
@ -21,7 +18,7 @@ cmdargs = gsa.getargs(
list( list(
bamlist = list(value=NA, doc="list of BAM files"), bamlist = list(value=NA, doc="list of BAM files"),
evalroot = list(value=NA, doc="VariantEval root"), evalroot = list(value=NA, doc="VariantEval root"),
tearxsout = list(value=NA, doc="Output path for tearsheet PDF"), tearout = list(value=NA, doc="Output path for tearsheet PDF"),
plotout = list(value=NA, doc="Output path for PDF") plotout = list(value=NA, doc="Output path for PDF")
), ),
doc="Creates a tearsheet" doc="Creates a tearsheet"
@ -44,7 +41,7 @@ for (bam in bamlist$V1) {
fclanes = c(fclanes, id); fclanes = c(fclanes, id);
} }
} else { } else {
cat(sprintf("Could not load '%s'\n", bam)); Print(sprintf("Could not load '%s'\n", bam));
} }
} }
@ -74,7 +71,7 @@ tearsheetdrop <- "tearsheetdrop.jpg" #put the path to the tearsheet backdrop her
tearsheet<-function(){ tearsheet<-function(){
pdf(file= cmdargs$statsout, width=22, height=15, pagecentre=TRUE, pointsize=24) pdf(file= cmdargs$tearout, width=22, height=15, pagecentre=TRUE, pointsize=24)
#define layout #define layout
layout(matrix(c(1,1,2,4,3,5), ncol=2, nrow=3, byrow=TRUE), heights=c(1, 2.5,2.5), respect=FALSE) layout(matrix(c(1,1,2,4,3,5), ncol=2, nrow=3, byrow=TRUE), heights=c(1, 2.5,2.5), respect=FALSE)
@ -94,7 +91,7 @@ tearsheet<-function(){
# Project summary # Project summary
projects = paste(unique(dproj$"Project"), collapse=", "); projects = paste(unique(dproj$"Project"), collapse=", ");
used_samples = length(unique(dproj$"External ID")); used_samples = length(bamlist$V1);
unused_samples = 0; unused_samples = 0;
@ -170,12 +167,18 @@ tearsheet<-function(){
par(mar=c(4,4,4,4)) par(mar=c(4,4,4,4))
textplot(table2, rmar=1, col.rownames="dark blue", cex=1.25) textplot(table2, rmar=1, col.rownames="dark blue", cex=1.25)
title(main="Bases Summary", family="sans", cex.main=1.75) title(main="Bases Summary", family="sans", cex.main=1.75)
cat("\nSequencing summary\n", file=cmdargs$statsout, append=TRUE);
# Sequencing summary # Sequencing summary
instrument = "Illumina GA2";#Can we get this? instrument <- c();
if(length(grep("AAXX", dproj$Flowcell))>0){
instrument <- c(instrument, "Illumina GA2")
}
if(length(grep("ABXX", dproj$Flowcell))>0){
instrument <- c(instrument, "Illumina HiSeq")
}
used_lanes = nrow(dproj); used_lanes = nrow(dproj);
unused_lanes_by_sequencing = 0; #can we get this? unused_lanes_by_sequencing = 0; #can we get this?
unused_lanes_by_analysis = 0; unused_lanes_by_analysis = 0;
@ -211,7 +214,7 @@ cat("\nSequencing summary\n", file=cmdargs$statsout, append=TRUE);
end_date = date[length(date)]; end_date = date[length(date)];
table3<-rbind(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)) 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(nrow(table3))
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 pariteies", "Read legnths", "Sequencing dates")