def drawCpuUsage(d,xat,xlbs,pic):
data=r.c(d)
pch = 22 # point like like a square
lty = 1 # line style solid line
col = "blue" # line color
ltype = "o" # line only http://stat.ethz.ch/R-manual/R-devel/library/graphics/html/plot.html
ylim = (0,100) # y domain
xaxis=1
yaxis=2
vertical_text=2
horizontal_text=1
text_size=0.8
yat=[x for x in range(0,110,10)]
ylbs=["%d%%"%x for x in yat]
legend_x=1
legend_y=100
# for r.text method
warn_val=40 # val over this value will display a text on point
xtext=[idx for idx,val in enumerate(d) if val > warn_val] # text x pos
ytext=[val for idx,val in enumerate(d) if val > warn_val] # text y pos
labtext=["%d%%"%val for idx,val in enumerate(d) if val > warn_val] # label for text
# summary
dmax=max(d)
sumry="max %.2f%%" % dmax
sumrycol="red" if dmax>50 else "green"
# plot
r.png(pic, width=900,height=450*0.6)
r.plot(data, type=ltype, col=col, ylim=ylim, pch=pch, lty=lty, axes=False, ann=False)
# draw text that over 40
# http://stat.ethz.ch/R-manual/R-devel/library/graphics/html/text.html
r.text(xtext, ytext, labels=labtext, pos=3, cex=0.8, col="red")
# summary text
r.mtext(sumry, side=3, cex=1, col=sumrycol)
# axis
r.axis(xaxis, las=vertical_text, at=xat, lab=r.c(xlbs))
r.axis(yaxis, las=horizontal_text, at=yat, lab=r.c(ylbs))
r.box()
# titles
r.title(main="CPU Sampling")
r.title(xlab="Time")
r.title(ylab="CPU Usage")
# reference line
# r.abline(h=50, col="gray") # at 50%
# legend
r.legend(legend_x, legend_y, r.c(("trunk")), col=col, cex=text_size, pch=pch, lty=lty)
r.dev_off()
def test():
data=r.c([1.25,3.45,6.75,20.2,9.9])
# draw image using rpy
r.png("test.png", width=300,height=300)
r.plot(data, type="o", col="blue", ylim=(0,100), pch=22, lty=1, axes=False, ann=False)
r.axis(1, at=(1,2,3,4,5), lab=r.c("a","b","c","d","e"))
r.axis(2, las=1, at=(0,50,100))
r.box()
r.title(main="CPU usage sampling result")
r.title(xlab="Time")
r.title(ylab="CPU")
r.legend(1,100,r.c("trunk"), cex=0.8, col=r.c("blue"), pch=22, lty=1)
r.dev_off()
def MK_fisher_pvalue(win_snp, win_div, AR_snp, AR_div):
if win_snp == 0 and win_div == 0 and AR_snp == 0 and AR_div == 0:
return 1.0
fisher_result = r.fisher_test(r.matrix(r.c([win_snp, win_div, AR_snp, AR_div]), nr=2))
return fisher_result['p.value']
def plot_one_boxplot_r(values, main="", logstring=""):
from rpy import r
if values.ndim == 1:
v = resize(values, (1, values.size))
else:
v = values
r.boxplot(v[0,:], xlim=[0,v.shape[0]+1], ylim=r.c(values.min(), values.max()), range=0, log=logstring,
main=main)
for i in range(1, v.shape[0]):
r.boxplot(v[i,:], at=i, add=True, range=0, log=logstring)
def MK_chi_pvalue(win_snp, win_div, AR_snp, AR_div):
chi_result = r.chisq_test(
r.matrix(r.c([win_snp, win_div, AR_snp, AR_div]), nr=2))
return chi_result['p.value']