%pylab inline
Populating the interactive namespace from numpy and matplotlib
WARNING: pylab import has clobbered these variables: ['f'] `%pylab --no-import-all` prevents importing * from pylab and numpy
import numpy
import matplotlib.collections as collections
font = {'family' : 'normal',
'size' : 16}
matplotlib.rc('font', **font)
def triptych(data):
# Two subplots, the axes array is 1-d
f, axarr = plt.subplots(3, sharex=True)
plot1, plot2, plot3 = axarr
plot1.plot(data[:,0], data[:,1], 'b-')
plot1.set_ylabel('CPU load (%)')
#axarr[0].set_title('Sharing X axis')
plot2.plot(data[:,0], data[:,2] / 1e6, 'r-')
plot2.set_ylabel('RAM (GB)')
plot3.plot(data[:,0], data[:,3] / 1000, 'g-')
plot3.set_ylabel('Disk (kTPS)')
plot3.set_xlabel('Time (seconds)')
f.set_size_inches(10, 8)
return f, axarr
import numpy
shortdata = numpy.loadtxt('short-m1.xlarge/log.out')
f, axarr = triptych(shortdata)
savefig('/tmp/shortdata-1.pdf')
f, axarr = triptych(shortdata)
plot1 = axarr[0]
plot1.set_ylim((0, 130))
plot1.annotate("QC", (300, 70))
plot1.annotate("diginorm", (700, 70))
plot1.annotate("assembly", (1400, 110))
plot1.annotate("annot", (1900, 80))
plot1.annotate("diff expr", (2300, 110))
savefig('/tmp/shortdata-2.pdf')
f, axarr = triptych(shortdata)
for p in axarr:
collection = collections.BrokenBarHCollection.span_where(
shortdata[:,0], ymin=0, ymax=1e11, where=(shortdata[:,0]>=521) & (shortdata[:,0]<1418), facecolor='green', alpha=0.3)
p.add_collection(collection)
collection = collections.BrokenBarHCollection.span_where(
shortdata[:,0], ymin=0, ymax=1e11, where=(shortdata[:,0]>=1418) & (shortdata[:,0]<1750), facecolor='red', alpha=0.3)
p.add_collection(collection)
plot1 = axarr[0]
plot1.set_ylim((0, 130))
plot1.annotate("diginorm", (700, 70))
plot1.annotate("assembly", (1400, 110))
savefig('/tmp/shortdata-3.pdf')
import numpy
longdata = numpy.loadtxt('m1.xlarge-normal/log.out')
f, axarr = triptych(longdata)
plot1 = axarr[0]
plot1.set_xticks([40000,80000,120000,160000])
plot1.set_ylim((0, 130))
plot1.annotate("QC", (20000, 50))
plot1.annotate("diginorm", (49362, 70))
plot1.annotate("assembly", (82001, 100))
plot2 = axarr[1]
for p in axarr:
collection = collections.BrokenBarHCollection.span_where(
longdata[:,0], ymin=0, ymax=1e11, where=(longdata[:,0]>=47362) & (longdata[:,0]<76741), facecolor='green', alpha=0.3)
p.add_collection(collection)
collection = collections.BrokenBarHCollection.span_where(
longdata[:,0], ymin=0, ymax=1e11, where=(longdata[:,0]>=76741), facecolor='red', alpha=0.3)
p.add_collection(collection)
savefig('/tmp/fig5.pdf')
import numpy
kmerdata = numpy.loadtxt('kmer-counting/log.out')
f, axarr = triptych(kmerdata)
plot1 = axarr[0]
plot1.set_ylim((0, 130))
plot1.annotate("Turtle", (0, 120))
plot1.annotate("DSK", (56, 110))
plot1.annotate("Tallymer", (246, 80))
plot1.annotate("khmer", (1666, 100))
plot1.annotate("Jellyfish", (2163, 110))
for p in axarr:
collection = collections.BrokenBarHCollection.span_where(
kmerdata[:,0], ymin=0, ymax=1e11, where=(kmerdata[:,0]>=0) & (kmerdata[:,0]<56), facecolor='green', alpha=0.3)
p.add_collection(collection)
collection = collections.BrokenBarHCollection.span_where(
kmerdata[:,0], ymin=0, ymax=1e11, where=(kmerdata[:,0]>=246) & (kmerdata[:,0]<1666), facecolor='red', alpha=0.3)
p.add_collection(collection)
collection = collections.BrokenBarHCollection.span_where(
kmerdata[:,0], ymin=0, ymax=1e11, where=(kmerdata[:,0]>=2163), facecolor='blue', alpha=0.3)
p.add_collection(collection)
savefig('/tmp/fig2.pdf')