zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Now uses PNGs and a very high downsampling value to more clearly display the information 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4928 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2011-01-03 13:57:51 +00:00
parent dba30c4118
commit 5583fa179b
1 changed files with 7 additions and 4 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

11
R/plot_GATK_performance_log.R
View File

@ -4,16 +4,16 @@ RUNME = T
onCMDLine = ! is.na(args[1])
DATA_FILE = args[1]
DESCRIPTION = args[2]
OUTPUT_PDF = paste(DATA_FILE, ".pdf", sep="")
#OUTPUT_PDF = paste(DATA_FILE, ".pdf", sep="")
MAX_POINTS = 1000
MAX_POINTS = 100000
if ( onCMDLine ) {
print(paste("Reading data from", DATA_FILE))
d = read.table(DATA_FILE, header=T)
}
if ( onCMDLine ) pdf(OUTPUT_PDF)
#if ( onCMDLine ) pdf(OUTPUT_PDF)
vec.margin <- function(x) {
l = length(x)
@ -43,24 +43,27 @@ generateOneReport <- function(d) {
qs = quantile(d$processing.speed, probs = c(0.01, 0.5, 0.99))
# unit processing time
if ( onCMDLine ) png(paste(DATA_FILE, ".speed.png", sep=""), width=1080, height=1080)
dpoints = everyNth(d, MAX_POINTS)
plot(dpoints$elapsed.time, dpoints$processing.speed, main=DESCRIPTION, xlab="Elapsed time (sec)", ylab="Processing speed (seconds per 1M units)", ylim=c(qs[1], qs[3]), type="b", col="cornflowerblue", lwd=2)
abline(h=qs[2], lty=2)
if ( onCMDLine ) dev.off()
# instantaneous processing speed
if ( onCMDLine ) png(paste(DATA_FILE, ".marginal.png", sep=""), width=1080, height=1080)
running_median_window = 101
rm = runmed(d$units.processed.margin, running_median_window)
POINT_COL = "#0000AA33"
plot(dpoints$elapsed.time, dpoints$units.processed.margin, main=DESCRIPTION, xlab="Elapsed time (sec)", ylab="Units processed in last timing interval", type="p", cex = 0.5, col=POINT_COL)
lines(d$elapsed.time, rm, lwd=3, col="red")
legend("topleft", c("Observations", "101-elt running median"), fill=c(POINT_COL, "red"))
if ( onCMDLine ) dev.off()
}
if ( RUNME ) {
generateOneReport(d)
}
if ( onCMDLine ) dev.off()