def make_emission_plot(self, gene_name, model):
plotting_info = []
for state in model.states:
if state.emissions is None:
assert state.name == 'init'
continue
plotting_info.append({})
plotting_info[-1]['name'] = state.name
plotting_info[-1]['nuke_freqs'] = state.emissions['probs']
paramutils.make_mutefreq_plot(self.base_plotdir + '/emissions', gene_name, plotting_info)
def make_emission_plot(self, gene_name, model):
plotting_info = []
for state in model.states:
if state.emissions is None:
assert state.name == 'init'
continue
plotting_info.append({
'name' : state.name,
'nuke_freqs' : state.emissions['probs'],
})
paramutils.make_mutefreq_plot(self.base_plotdir + '/emissions', gene_name, plotting_info, debug=True)
def make_emission_plot(self, gene_name, model):
plotting_info = []
for state in model.states:
if len(state.emissions) == 0:
assert state.name == 'init'
continue
plotting_info.append({})
plotting_info[-1]['name'] = state.name
plotting_info[-1]['nuke_freqs'] = state.emissions['probs']
paramutils.make_mutefreq_plot(self.base_plotdir + '/emissions',
gene_name, plotting_info)
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,
only_csv=False,
only_overall=False,
make_per_base_plots=False):
import plotting
if not self.finalized:
self.finalize()
overall_plotdir = plotdir + '/overall'
for gene in self.freqs:
if only_overall:
continue
freqs = self.freqs[gene]
if len(freqs) == 0:
if gene not in glutils.dummy_d_genes.values():
print ' %s no mutefreqer obs for %s' % (utils.color(
'red', 'warning'), utils.color_gene(gene))
continue
sorted_positions = sorted(freqs.keys())
genehist = Hist(sorted_positions[-1] - sorted_positions[0] + 1,
sorted_positions[0] - 0.5,
sorted_positions[-1] + 0.5,
xtitle='position',
ytitle='mut freq',
title=gene)
for position in sorted_positions:
hi_diff = abs(freqs[position]['freq'] -
freqs[position]['freq_hi_err'])
lo_diff = abs(freqs[position]['freq'] -
freqs[position]['freq_lo_err'])
err = 0.5 * (hi_diff + lo_diff)
genehist.set_ibin(genehist.find_bin(position),
freqs[position]['freq'],
error=err)
xline = None
figsize = [7, 4]
if utils.get_region(gene) in utils.conserved_codons[
self.glfo['locus']]:
xline = utils.cdn_pos(self.glfo, utils.get_region(gene), gene)
if utils.get_region(gene) == 'v':
figsize[0] *= 3.5
elif utils.get_region(gene) == 'j':
figsize[0] *= 2
plotting.draw_no_root(self.per_gene_mean_rates[gene],
plotdir=plotdir + '/per-gene/' +
utils.get_region(gene),
plotname=utils.sanitize_name(gene),
errors=True,
write_csv=True,
only_csv=only_csv,
shift_overflows=True)
# per-position plots:
plotting.draw_no_root(genehist,
plotdir=plotdir + '/per-gene-per-position/' +
utils.get_region(gene),
plotname=utils.sanitize_name(gene),
errors=True,
write_csv=True,
xline=xline,
figsize=figsize,
only_csv=only_csv,
shift_overflows=True)
if make_per_base_plots:
# per-position, per-base plots: (super slow, so commented by default)
import paramutils
plotting_info = []
for pos in sorted_positions:
plotting_info.append({
'name':
str(pos), # not sure if this is right, but I think so
'nuke_freqs': {n: freqs[pos][n]
for n in utils.nukes},
'gl_nuke':
utils.gseq(self.glfo, gene)[pos],
})
paramutils.make_mutefreq_plot(
plotdir + '/' + utils.get_region(gene) + '-per-base',
utils.sanitize_name(gene), plotting_info)
# make mean mute freq hists
for rstr in ['all', 'cdr3'] + utils.regions:
if rstr == 'all':
bounds = (0.0, 0.4)
else:
bounds = (0.0, 0.6 if rstr == 'd' else 0.4)
plotting.draw_no_root(self.mean_rates[rstr],
plotname=rstr + '_mean-freq',
plotdir=overall_plotdir,
stats='mean',
bounds=bounds,
write_csv=True,
only_csv=only_csv,
shift_overflows=True)
plotting.draw_no_root(self.mean_n_muted[rstr],
plotname=rstr + '_mean-n-muted',
plotdir=overall_plotdir,
stats='mean',
write_csv=True,
only_csv=only_csv,
shift_overflows=True)
if not only_csv: # write html file and fix permissiions
for substr in self.subplotdirs:
plotting.make_html(plotdir + '/' + substr)
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
