def drawCompareN50Plot( options, xsamples, ysamples ):
#Sort xsamples and ysamples in the order of the sampleNames:
xsamples = sorted( xsamples, key=lambda s: s.attrib[ 'sampleName' ] )
if len(xsamples) < 1 or len(ysamples) < 1:
return
xrefname = xsamples[0].attrib[ 'referenceName' ]
yrefname = ysamples[0].attrib[ 'referenceName' ]
options.out = os.path.join( options.outdir, options.prefix + '_' + xrefname + '_' + yrefname )
fig, pdf = libplot.initImage( 8.0, 8.0, options )
axes = fig.add_axes( [0.12, 0.1, 0.85, 0.85] )
lines, lineNames, maxval, minval = drawCompareN50data( axes, xsamples, ysamples, options )
if len(lines) == 0:
sys.stderr.write('Comparing N50 stats of %s and %s: All values are 0, no plot created\n' %(xrefname, yrefname) )
return
title = "N50" #% ( libplot.properName(xrefname), libplot.properName(yrefname) )
axes.set_title(title)
#Legend
fontP = FontProperties()
fontP.set_size( 'small' )
box = axes.get_position()
axes.set_position( [box.x0, box.y0, box.width*0.8, box.height*0.8] )
legend = pyplot.legend( lines, lineNames, numpoints=1, prop=fontP, loc="best", bbox_to_anchor=(1, 0.5) )
legend._drawFrame = False
libplot.setTicks( axes )
span = maxval - minval
axes.set_xlim( minval - span*0.1, maxval + span*0.1 )
axes.set_ylim( minval - span*0.1, maxval + span*0.1 )
libplot.writeImage( fig, pdf, options )
def drawContiguityPlot( options, stats ):
#options.out = os.path.join(options.outdir, "contiguity_" + stats.refname) #name of output file
options.out = os.path.join(options.outdir, options.exp + "_" + stats.refname) #name of output file
if options.includeCov:
options.out = options.out + "_incCov"
options.ycutoff = 0.7 #HACK
else:#HACK
options.ycutoff = 0.95 #HACK
fig, pdf = libplot.initImage( 8.0, 10.0, options )
axes = libplot.setAxes( fig )
lines, sampleNames, ymin = drawData( axes, stats, options )
drawLegend( axes, lines, sampleNames, options )
if options.ycutoff:
setAxisLimits( axes, options.ycutoff )
else:
setAxisLimits( axes, ymin*0.98 )
libplot.setTicks( axes )
libplot.writeImage( fig, pdf, options )
def drawCompareData( axesList, xstats, ystats, options ):
#Only draw the overlapped samples:
#colors = libplot.getColors2( len(xstats) )
colors = libplot.getColors1()
#colorindex = -1
#colorindex = 0
colorindex = 1
lines = []
sampleNames = []
p0axes = axesList[0] #plot 0 axes (see def 'setCompareAxes')
aggData = [] #data points (buckets) of all samples
minval = float('inf')
for xsample in xstats:
ysample = getSample( ystats, xsample.name )
if ysample is None:
continue
xsample, ysample = intersect(xsample, ysample)
#if len(xsample) != len(ysample):
# xsample, ysample = intersect(xsample, ysample)
# sys.stderr.write( "Error: Two xml files do not have the same number of buckets for sample %s\n" % xsample.name )
#sys.exit( 1 )
data = [] #list of (x,y) tuples
colorindex += 1
for i in range( len( xsample ) ): #each bucket
if xsample[i].mid != ysample[i].mid:
sys.stderr.write( "Two xml files have different buckets\n " )
sys.exit( 1 )
if options.includeCov:
data.append( (xsample[i].correctPerSample, ysample[i].correctPerSample) )
else:
data.append( (xsample[i].correctPerAligned, ysample[i].correctPerAligned) )
x2data = [ point[0] for point in data ]
y2data = [ point[1] for point in data ]
l = p0axes.plot( x2data, y2data, color=colors[colorindex], marker='.', markersize=4.0, linestyle='none' )
lines.append( l )
sampleNames.append( xsample.name )
aggData.extend( data )
minval = min( [min(x2data), min(y2data)] )
#Draw the y=x line
x = [0, 1]
y = [0, 1]
p0axes.plot(x, y, color="#919191")
fontP = FontProperties()
fontP.set_size('small')
libplot.editSpine( p0axes )
p0axes.set_title(options.title)
p0axes.set_xlabel( libplot.properName(xstats.refname) )
p0axes.set_ylabel( libplot.properName(ystats.refname) )
libplot.setTicks( p0axes )
for l in p0axes.xaxis.get_ticklabels():
l.set_fontsize('small')
for l in p0axes.yaxis.get_ticklabels():
l.set_fontsize('small')
#legend:
legend = p0axes.legend( lines, [ libplot.properName(n) for n in sampleNames], 'lower right', numpoints = 1, prop=fontP, ncol = 2)
legend._drawFrame = False
#p0axes.set_xlim( -0.005, 1.005 )
#p0axes.set_ylim( -0.005, 1.005 )
ycutoff = minval
if options.ycutoff:
ycutoff = options.ycutoff
p0axes.set_xlim( ycutoff - (1-ycutoff)*0.02, 1 + (1 - ycutoff)*0.01 )
p0axes.set_ylim( ycutoff - (1-ycutoff)*0.02, 1 + (1 - ycutoff)*0.01 )
#box = p0axes.get_position()
#p0axes.set_position([box.x0, box.y0, box.width * 0.8, box.height * 0.8])
#legend = pyplot.legend( lines, sampleNames, numpoints = 1, prop= fontP, loc="best", bbox_to_anchor=(1, 0.6))
#legend._drawFrame=False
#DRAW AGGREGATE DATA (plot 1 and plot 2):
nbins = 20
p1axes = axesList[1]
y1min, y1max = drawAggData( p1axes, aggData, 0, 0, 1, ycutoff, nbins )
y1lim = max( abs(y1min), abs(y1max) )
p1axes.set_ylim( -y1lim*1.1, y1lim*1.1 )
p1axes.set_xlim( ycutoff - (1-ycutoff)*0.02, 1 + (1-ycutoff)*0.01 )
#p1axes.set_ylim( y1min*1.1, y1max*1.1 )
for loc, spine in p1axes.spines.iteritems():
if loc == 'left':
spine.set_position( ( 'outward', 10 ) )
spine.set_color( 'none' )
p1axes.axhline( 0, color = '#000000' )
p1axes.xaxis.set_major_locator( NullLocator() )
p1axes.xaxis.set_major_formatter( NullFormatter() )
p1axes.yaxis.set_ticks([-y1lim, 0, y1lim])
for l in p1axes.yaxis.get_ticklabels():
l.set_fontsize('small')
p2axes = axesList[2]
x2min, x2max = drawAggData( p2axes, aggData, 1, 0, 1, ycutoff, nbins )
x2lim = max( abs(x2min), abs(x2max) )
p2axes.set_xlim( -x2lim*1.1, x2lim*1.1 )
p2axes.set_ylim( ycutoff - (1-ycutoff)*0.02, 1 + (1- ycutoff)*0.01 )
#p2axes.set_xlim( x2min*1.1, x2max*1.1 )
for loc, spine in p2axes.spines.iteritems():
if loc == 'bottom':
spine.set_position( ( 'outward', 10 ) )
spine.set_color( 'none' )
p2axes.axvline( 0, color = '#000000' )
p2axes.yaxis.set_major_locator( NullLocator() )
p2axes.yaxis.set_major_formatter( NullFormatter() )
p2axes.xaxis.set_ticks([-x2lim, 0, x2lim])
for l in p2axes.xaxis.get_ticklabels():
l.set_fontsize('small')
l.set_rotation( 45 )
return