def plot(self, base_plotdir, cyst_positions=None, tryp_positions=None):
if not self.finalized:
self.finalize()
plotdir = base_plotdir + '/mute-freqs'
utils.prep_dir(plotdir + '/plots', multilings=('*.csv', '*.svg'))
for region in utils.regions:
utils.prep_dir(plotdir + '/' + region + '/plots', multilings=('*.csv', '*.svg'))
utils.prep_dir(plotdir + '/' + region + '-per-base/plots', multilings=('*.csv', '*.png'))
for gene in self.counts:
counts, plotting_info = self.counts[gene], self.plotting_info[gene]
sorted_positions = sorted(counts)
hist = TH1D('hist_' + utils.sanitize_name(gene), '',
sorted_positions[-1] - sorted_positions[0] + 1,
sorted_positions[0] - 0.5, sorted_positions[-1] + 0.5)
for position in sorted_positions:
hist.SetBinContent(hist.FindBin(position), counts[position]['freq'])
hi_diff = abs(counts[position]['freq'] - counts[position]['freq_hi_err'])
lo_diff = abs(counts[position]['freq'] - counts[position]['freq_lo_err'])
err = 0.5*(hi_diff + lo_diff)
hist.SetBinError(hist.FindBin(position), err)
plotfname = plotdir + '/' + utils.get_region(gene) + '/plots/' + utils.sanitize_name(gene) + '.svg'
xline = None
if utils.get_region(gene) == 'v' and cyst_positions is not None:
xline = cyst_positions[gene]['cysteine-position']
elif utils.get_region(gene) == 'j' and tryp_positions is not None:
xline = int(tryp_positions[gene])
plotting.draw(hist, 'int', plotdir=plotdir + '/' + utils.get_region(gene), plotname=utils.sanitize_name(gene), errors=True, write_csv=True, xline=xline, draw_str='e') #, cwidth=4000, cheight=1000)
paramutils.make_mutefreq_plot(plotdir + '/' + utils.get_region(gene) + '-per-base', utils.sanitize_name(gene), plotting_info)
# for region in utils.regions:
# utils.prep_dir(plotdir + '/' + region + '/tmp/plots', multilings=('*.csv', '*.svg'))
# for gene in self.tmpcounts:
# for position in self.tmpcounts[gene]:
# roothist = plotting.make_hist_from_my_hist_class(self.tmpcounts[gene][position]['muted'], gene + '_' + str(position))
# plotting.draw(roothist, 'int', plotdir=plotdir + '/' + utils.get_region(gene) + '/tmp', plotname=utils.sanitize_name(gene) + '_' + str(position), errors=True, write_csv=True) #, cwidth=4000, cheight=1000)
# make mean mute freq hists
hist = plotting.make_hist_from_my_hist_class(self.mean_rates['all'], 'all-mean-freq')
plotting.draw(hist, 'float', plotname='all-mean-freq', plotdir=plotdir, stats='mean', bounds=(0.0, 0.4), write_csv=True)
for region in utils.regions:
hist = plotting.make_hist_from_my_hist_class(self.mean_rates[region], region+'-mean-freq')
plotting.draw(hist, 'float', plotname=region+'-mean-freq', plotdir=plotdir, stats='mean', bounds=(0.0, 0.4), write_csv=True)
check_call(['./bin/makeHtml', plotdir, '3', 'null', 'svg'])
# then write html file and fix permissiions
for region in utils.regions:
check_call(['./bin/makeHtml', plotdir + '/' + region, '1', 'null', 'svg'])
check_call(['./bin/makeHtml', plotdir + '/' + region + '-per-base', '1', 'null', 'png'])
check_call(['./bin/permissify-www', plotdir]) # NOTE this should really permissify starting a few directories higher up
def plot(self, plotdir):
utils.prep_dir(plotdir + '/plots', wildling=None, multilings=['*.csv', '*.svg', '*.root'])
for column in self.values:
if self.only_correct_gene_fractions and column not in bool_columns:
continue
if column in bool_columns:
right = self.values[column]['right']
wrong = self.values[column]['wrong']
errs = fraction_uncertainty.err(right, right+wrong)
print ' %s\n correct up to allele: %4d / %-4d = %4.4f (-%.3f, +%.3f)' % (column, right, right+wrong, float(right) / (right + wrong), errs[0], errs[1])
hist = plotting.make_bool_hist(right, wrong, self.name + '-' + column)
plotting.draw(hist, 'bool', plotname=column, plotdir=plotdir, write_csv=True)
else:
# TODO this is dumb... I should make the integer-valued ones histograms as well
hist = plotting.make_hist_from_dict_of_counts(self.values[column], 'int', self.name + '-' + column, normalize=True)
log = ''
if column.find('hamming_to_true_naive') >= 0:
hist.GetXaxis().SetTitle('hamming distance')
else:
hist.GetXaxis().SetTitle('inferred - true')
plotting.draw(hist, 'int', plotname=column, plotdir=plotdir, write_csv=True, log=log)
for column in self.hists:
hist = plotting.make_hist_from_my_hist_class(self.hists[column], column)
plotting.draw(hist, 'float', plotname=column, plotdir=plotdir, write_csv=True, log=log)
check_call(['./bin/makeHtml', plotdir, '3', 'null', 'svg'])
check_call(['./bin/permissify-www', plotdir]) # NOTE this should really permissify starting a few directories higher up
def plot(self):
for column in self.values:
if column in bool_columns:
right = self.values[column]['right']
wrong = self.values[column]['wrong']
print ' %s\n correct up to allele: %4d / %-4d = %4.2f' % (column, right, right+wrong, float(right) / (right + wrong))
hist = plotting.make_bool_hist(right, wrong, self.name + '-' + column)
plotting.draw(hist, 'bool', plotname=column, plotdir=self.plotdir, write_csv=True)
else:
hist = plotting.make_hist_from_dict_of_counts(self.values[column], 'int', self.name + '-' + column, normalize=True)
log = ''
if column.find('hamming_to_true_naive') >= 0:
hist.GetXaxis().SetTitle('hamming distance')
else:
hist.GetXaxis().SetTitle('inferred - true')
plotting.draw(hist, 'int', plotname=column, plotdir=self.plotdir, write_csv=True, log=log)
for column in self.hists:
hist = plotting.make_hist_from_my_hist_class(self.hists[column], 'mute_freqs')
plotting.draw(hist, 'float', plotname=column, plotdir=self.plotdir, write_csv=True, log=log)
check_call(['./bin/makeHtml', self.plotdir, '3', 'null', 'svg'])
check_call(['./bin/permissify-www', self.plotdir]) # NOTE this should really permissify starting a few directories higher up
def plot(self, base_plotdir, cyst_positions=None, tryp_positions=None):
if not self.finalized:
self.finalize()
plotdir = base_plotdir + '/mute-freqs'
utils.prep_dir(plotdir + '/plots', multilings=('*.csv', '*.svg'))
for region in utils.regions:
utils.prep_dir(plotdir + '/' + region + '/plots',
multilings=('*.csv', '*.svg'))
utils.prep_dir(plotdir + '/' + region + '-per-base/plots',
multilings=('*.csv', '*.png'))
for gene in self.counts:
counts, plotting_info = self.counts[gene], self.plotting_info[gene]
sorted_positions = sorted(counts)
hist = TH1D('hist_' + utils.sanitize_name(gene), '',
sorted_positions[-1] - sorted_positions[0] + 1,
sorted_positions[0] - 0.5, sorted_positions[-1] + 0.5)
for position in sorted_positions:
hist.SetBinContent(hist.FindBin(position),
counts[position]['freq'])
hi_diff = abs(counts[position]['freq'] -
counts[position]['freq_hi_err'])
lo_diff = abs(counts[position]['freq'] -
counts[position]['freq_lo_err'])
err = 0.5 * (hi_diff + lo_diff)
hist.SetBinError(hist.FindBin(position), err)
plotfname = plotdir + '/' + utils.get_region(
gene) + '/plots/' + utils.sanitize_name(gene) + '.svg'
xline = None
if utils.get_region(gene) == 'v' and cyst_positions is not None:
xline = cyst_positions[gene]['cysteine-position']
elif utils.get_region(gene) == 'j' and tryp_positions is not None:
xline = int(tryp_positions[gene])
plotting.draw(hist,
'int',
plotdir=plotdir + '/' + utils.get_region(gene),
plotname=utils.sanitize_name(gene),
errors=True,
write_csv=True,
xline=xline,
draw_str='e') #, cwidth=4000, cheight=1000)
paramutils.make_mutefreq_plot(
plotdir + '/' + utils.get_region(gene) + '-per-base',
utils.sanitize_name(gene), plotting_info)
# make mean mute freq hists
hist = plotting.make_hist_from_my_hist_class(self.mean_rates['all'],
'all-mean-freq')
plotting.draw(hist,
'float',
plotname='all-mean-freq',
plotdir=plotdir,
stats='mean',
bounds=(0.0, 0.4),
write_csv=True)
for region in utils.regions:
hist = plotting.make_hist_from_my_hist_class(
self.mean_rates[region], region + '-mean-freq')
plotting.draw(hist,
'float',
plotname=region + '-mean-freq',
plotdir=plotdir,
stats='mean',
bounds=(0.0, 0.4),
write_csv=True)
check_call(['./bin/makeHtml', plotdir, '3', 'null', 'svg'])
# then write html file and fix permissiions
for region in utils.regions:
check_call(
['./bin/makeHtml', plotdir + '/' + region, '1', 'null', 'svg'])
check_call([
'./bin/makeHtml', plotdir + '/' + region + '-per-base', '1',
'null', 'png'
])
check_call(
['./bin/permissify-www', plotdir]
) # NOTE this should really permissify starting a few directories higher up
