def hist_ORF_CDS_logscale(self,
alpha=0.5,
bins=40,
xlabel="Length",
ylabel="#"):
self.hist_ORF_CDS_linearscale(alpha, bins, xlabel, ylabel)
pylab.yscale("log")
def hist_ZMW_subreads(self,
alpha=0.5,
hold=False,
fontsize=12,
grid=True,
xlabel="Number of ZMW passes",
ylabel="#",
label="",
title="Number of ZMW passes"):
"""Plot histogram of number of reads per ZMW (number of passes)
:param float alpha: transparency of the histograms
:param bool hold:
:param int fontsize:
:param bool grid:
:param str xlabel:
:param str ylabel:
:param str label: label of the histogram (for the legend)
:param str title:
.. plot::
:include-source:
from sequana.pacbio import BAMPacbio
from sequana import sequana_data
b = BAMPacbio(sequana_data("test_pacbio_subreads.bam"))
b.hist_ZMW_subreads()
"""
if self._nb_pass is None:
self._get_ZMW_passes()
max_nb_pass = max(self._nb_pass.keys())
k = range(1, max_nb_pass + 1)
val = [self._nb_pass[i] for i in k]
# histogram nb passes
if hold is False:
pylab.clf()
pylab.bar(k, val, alpha=alpha, label=label)
if len(k) < 5:
pylab.xticks(range(6), range(6))
pylab.xlabel(xlabel, fontsize=fontsize)
pylab.ylabel(ylabel, fontsize=fontsize)
pylab.yscale('log')
pylab.title(title, fontsize=fontsize)
if grid is True:
pylab.grid(True)
def hist_ZMW_subreads(self, hold=False, fontsize=12,
grid=True,xlabel="Number of ZMW passes",ylabel="#"):
"""
Plot histogram of number of reads per ZMW
"""
if self._nb_pass is None:
self._get_ZMW_passes()
max_nb_pass = max(self._nb_pass.keys())
k = range(1,max_nb_pass+1)
val = [self._nb_pass[i] for i in k]
# histogram nb passes
if hold is False:
pylab.clf()
pylab.hist(k, weights=val, bins=max_nb_pass)
pylab.xlabel(xlabel, fontsize=fontsize)
pylab.ylabel(ylabel, fontsize=fontsize)
pylab.yscale('log')
pylab.title("Number of ZMW passes",fontsize=fontsize)
if grid is True:
pylab.grid(True)
def hist_ORF_CDS_logscale(self, alpha=0.5, bins=40, xlabel="Length", ylabel="#"):
self.hist_ORF_CDS_linearscale(alpha, bins, xlabel, ylabel)
pylab.yscale("log")