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gatk-3.8
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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
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11
R/plot_GATK_performance_log.R
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@ -4,16 +4,16 @@ RUNME = T
onCMDLine = ! is.na(args[1]) onCMDLine = ! is.na(args[1])
DATA_FILE = args[1] DATA_FILE = args[1]
DESCRIPTION = args[2] 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 ) { if ( onCMDLine ) {
print(paste("Reading data from", DATA_FILE)) print(paste("Reading data from", DATA_FILE))
d = read.table(DATA_FILE, header=T) d = read.table(DATA_FILE, header=T)
} }
if ( onCMDLine ) pdf(OUTPUT_PDF) #if ( onCMDLine ) pdf(OUTPUT_PDF)
vec.margin <- function(x) { vec.margin <- function(x) {
l = length(x) l = length(x)
@ -43,24 +43,27 @@ generateOneReport <- function(d) {
qs = quantile(d$processing.speed, probs = c(0.01, 0.5, 0.99)) qs = quantile(d$processing.speed, probs = c(0.01, 0.5, 0.99))
# unit processing time # unit processing time
if ( onCMDLine ) png(paste(DATA_FILE, ".speed.png", sep=""), width=1080, height=1080)
dpoints = everyNth(d, MAX_POINTS) 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) 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) abline(h=qs[2], lty=2)
if ( onCMDLine ) dev.off()
# instantaneous processing speed # instantaneous processing speed
if ( onCMDLine ) png(paste(DATA_FILE, ".marginal.png", sep=""), width=1080, height=1080)
running_median_window = 101 running_median_window = 101
rm = runmed(d$units.processed.margin, running_median_window) rm = runmed(d$units.processed.margin, running_median_window)
POINT_COL = "#0000AA33" 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) 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$elapsed.time, rm, lwd=3, col="red") lines(d$elapsed.time, rm, lwd=3, col="red")
legend("topleft", c("Observations", "101-elt running median"), fill=c(POINT_COL, "red")) legend("topleft", c("Observations", "101-elt running median"), fill=c(POINT_COL, "red"))
if ( onCMDLine ) dev.off()
} }
if ( RUNME ) { if ( RUNME ) {
generateOneReport(d) generateOneReport(d)
} }
if ( onCMDLine ) dev.off()