diff --git a/R/DataProcessingReport/GetTearsheetStats.R b/R/DataProcessingReport/GetTearsheetStats.R index ee5fd6909..68f6468c2 100644 --- a/R/DataProcessingReport/GetTearsheetStats.R +++ b/R/DataProcessingReport/GetTearsheetStats.R @@ -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)