def make_transition_plot(self, gene_name, model):
""" NOTE shares a lot with make_mutefreq_plot() in python/paramutils.py """
fig, ax = plotting.mpl_init()
fig.set_size_inches(plotting.plot_ratios[utils.get_region(gene_name)])
ibin = 0
print utils.color_gene(utils.unsanitize_name(gene_name))
legend_colors = set() # add a color to this the first time you plot it
for state in model.states:
# bin label
ax.text(-0.5 + ibin, -0.075, paramutils.simplify_state_name(state.name), rotation='vertical', size=8)
sorted_to_states = {}
for name in state.transitions.keys():
if name.find('IG') == 0 or name.find('TR') == 0:
sorted_to_states[name] = int(paramutils.simplify_state_name(name))
else:
sorted_to_states[name] = name
sorted_to_states = sorted(sorted_to_states.items(), key=operator.itemgetter(1))
total = 0.0
for to_state, simple_to_state in sorted_to_states:
prob = state.transitions[to_state]
alpha = 0.6
width = 3
if 'insert' in str(simple_to_state):
label = 'insert'
color = '#3498db' # blue
elif str(simple_to_state) == 'end':
label = 'end'
color = 'red'
else: # regional/internal states
assert to_state.find('IG') == 0 or to_state.find('TR') == 0
label = 'internal'
color = 'green'
label_to_use = None
if color not in legend_colors:
label_to_use = label
legend_colors.add(color)
# horizontal line at height total+prob
ax.plot([-0.5 + ibin, 0.5 + ibin], [total + prob, total + prob], color=color, linewidth=width, alpha=alpha, label=label_to_use)
# vertical line from total to total + prob
ax.plot([ibin, ibin], [total + 0.01, total + prob], color=color, alpha=alpha, linewidth=width)
midpoint = 0.5*(prob + 2*total)
# ax.text(ibin, midpoint, paramutils.simplify_state_name(to_state)) # nicely labels the midpoint of the chunk between lines, but there isn't really room for it
total += prob
ibin += 1
ax.get_xaxis().set_visible(False)
plotting.mpl_finish(ax, self.base_plotdir + '/transitions', gene_name, ybounds=(-0.01, 1.01), xbounds=(-3, len(model.states) + 3), leg_loc=(0.95, 0.1), adjust={'left' : 0.1, 'right' : 0.8}, leg_prop={'size' : 8})
def make_transition_plot(self, gene_name, model):
""" NOTE shares a lot with make_mutefreq_plot() in python/paramutils.py """
fig, ax = plotting.mpl_init()
fig.set_size_inches(plotting.plot_ratios[utils.get_region(gene_name)])
ibin = 0
print utils.color_gene(utils.unsanitize_name(gene_name))
legend_colors = set() # add a color to this the first time you plot it
for state in model.states:
# bin label
ax.text(-0.5 + ibin, -0.075, paramutils.simplify_state_name(state.name), rotation='vertical', size=8)
sorted_to_states = {}
for name in state.transitions.keys():
if name.find('IG') == 0:
sorted_to_states[name] = int(paramutils.simplify_state_name(name))
else:
sorted_to_states[name] = name
sorted_to_states = sorted(sorted_to_states.items(), key=operator.itemgetter(1))
total = 0.0
for to_state, simple_to_state in sorted_to_states:
prob = state.transitions[to_state]
alpha = 0.6
width = 3
if 'insert' in str(simple_to_state):
label = 'insert'
color = '#3498db' # blue
elif str(simple_to_state) == 'end':
label = 'end'
color = 'red'
else: # regional/internal states
assert to_state.find('IG') == 0
label = 'internal'
color = 'green'
label_to_use = None
if color not in legend_colors:
label_to_use = label
legend_colors.add(color)
# horizontal line at height total+prob
ax.plot([-0.5 + ibin, 0.5 + ibin], [total + prob, total + prob], color=color, linewidth=width, alpha=alpha, label=label_to_use)
# vertical line from total to total + prob
ax.plot([ibin, ibin], [total + 0.01, total + prob], color=color, alpha=alpha, linewidth=width)
midpoint = 0.5*(prob + 2*total)
# ax.text(ibin, midpoint, paramutils.simplify_state_name(to_state)) # nicely labels the midpoint of the chunk between lines, but there isn't really room for it
total += prob
ibin += 1
ax.get_xaxis().set_visible(False)
plotting.mpl_finish(ax, self.base_plotdir + '/transitions', gene_name, ybounds=(-0.01, 1.01), xbounds=(-3, len(model.states) + 3), leg_loc=(0.95, 0.1), adjust={'left' : 0.1, 'right' : 0.8}, leg_prop={'size' : 8})
def make_transition_plot(self, gene_name, model):
ibin = 0
drawn_name_texts, lines, texts = {}, {}, {}
for state in model.states:
if utils.get_region(gene_name) in self.skip_boring_states:
if state.name != 'init' and len(state.transitions) == 1: # skip uninteresting states
to_state = state.transitions.keys()[0] # skip states with only transitions to end
if to_state == 'end':
continue
if find_state_number(state.name) + 1 == find_state_number(to_state): # skip states with only transitions to next state
continue
drawn_name_texts[state.name] = TPaveText(-0.5 + ibin, -0.1, 0.5 + ibin, -0.05)
drawn_name_texts[state.name].SetBorderSize(0)
drawn_name_texts[state.name].SetFillColor(0)
drawn_name_texts[state.name].SetFillStyle(0)
drawn_name_texts[state.name].AddText(-0.5 + ibin, -0.075, paramutils.simplify_state_name(state.name))
sorted_to_states = {}
for name in state.transitions.keys():
if name.find('IGH') == 0:
sorted_to_states[name] = int(paramutils.simplify_state_name(name))
else:
sorted_to_states[name] = name
sorted_to_states = sorted(sorted_to_states.items(), key=operator.itemgetter(1))
total = 0.0
lines[state.name], texts[state.name] = [], []
for to_state, simple_to_state in sorted_to_states:
prob = state.transitions[to_state]
lines[state.name].append(TLine(-0.5 + ibin, total + prob, 0.5 + ibin, total + prob))
lines[state.name][-1].SetLineColor(kGreen+2)
lines[state.name][-1].SetLineWidth(6)
midpoint = 0.5*(prob + 2*total)
texts[state.name].append(TPaveText(-0.5 + ibin, midpoint-0.04, 0.5 + ibin, midpoint + 0.01))
texts[state.name][-1].AddText(-0.5 + ibin, midpoint, paramutils.simplify_state_name(to_state))
texts[state.name][-1].SetBorderSize(0)
texts[state.name][-1].SetFillColor(0)
texts[state.name][-1].SetFillStyle(0)
total += prob
ibin += 1
cvn = TCanvas('mod-cvn', '', 1000, 400)
n_bins = ibin
hframe = TH1D(model.name + '-transition-frame', utils.unsanitize_name(model.name), n_bins, -0.5, n_bins - 0.5)
if utils.get_region(gene_name) in self.skip_boring_states:
hframe.SetTitle(hframe.GetTitle() + ' (skipped boring states)')
hframe.SetNdivisions(202, 'y')
hframe.SetNdivisions(0, 'x')
hframe.Draw()
for state_name in lines.keys():
drawn_name_texts[state_name].Draw()
for itrans in range(len(lines[state_name])):
lines[state_name][itrans].Draw()
texts[state_name][itrans].Draw()
cvn.SaveAs(self.base_plotdir + '/transitions/plots/' + gene_name + '.png')
def make_transition_plot(self, gene_name, model):
ibin = 0
drawn_name_texts, lines, texts = {}, {}, {}
for state in model.states:
if utils.get_region(gene_name) in self.skip_boring_states:
if state.name != 'init' and len(
state.transitions) == 1: # skip uninteresting states
to_state = state.transitions.keys()[
0] # skip states with only transitions to end
if to_state == 'end':
continue
if find_state_number(state.name) + 1 == find_state_number(
to_state
): # skip states with only transitions to next state
continue
drawn_name_texts[state.name] = TPaveText(-0.5 + ibin, -0.1,
0.5 + ibin, -0.05)
drawn_name_texts[state.name].SetBorderSize(0)
drawn_name_texts[state.name].SetFillColor(0)
drawn_name_texts[state.name].SetFillStyle(0)
drawn_name_texts[state.name].AddText(
-0.5 + ibin, -0.075,
paramutils.simplify_state_name(state.name))
sorted_to_states = {}
for name in state.transitions.keys():
if name.find('IGH') == 0:
sorted_to_states[name] = int(
paramutils.simplify_state_name(name))
else:
sorted_to_states[name] = name
sorted_to_states = sorted(sorted_to_states.items(),
key=operator.itemgetter(1))
total = 0.0
lines[state.name], texts[state.name] = [], []
for to_state, simple_to_state in sorted_to_states:
prob = state.transitions[to_state]
lines[state.name].append(
TLine(-0.5 + ibin, total + prob, 0.5 + ibin, total + prob))
lines[state.name][-1].SetLineColor(kGreen + 2)
lines[state.name][-1].SetLineWidth(6)
midpoint = 0.5 * (prob + 2 * total)
texts[state.name].append(
TPaveText(-0.5 + ibin, midpoint - 0.04, 0.5 + ibin,
midpoint + 0.01))
texts[state.name][-1].AddText(
-0.5 + ibin, midpoint,
paramutils.simplify_state_name(to_state))
texts[state.name][-1].SetBorderSize(0)
texts[state.name][-1].SetFillColor(0)
texts[state.name][-1].SetFillStyle(0)
total += prob
ibin += 1
cvn = TCanvas('mod-cvn', '', 1000, 400)
n_bins = ibin
hframe = TH1D(model.name + '-transition-frame',
utils.unsanitize_name(model.name), n_bins, -0.5,
n_bins - 0.5)
if utils.get_region(gene_name) in self.skip_boring_states:
hframe.SetTitle(hframe.GetTitle() + ' (skipped boring states)')
hframe.SetNdivisions(202, 'y')
hframe.SetNdivisions(0, 'x')
hframe.Draw()
for state_name in lines.keys():
drawn_name_texts[state_name].Draw()
for itrans in range(len(lines[state_name])):
lines[state_name][itrans].Draw()
texts[state_name][itrans].Draw()
cvn.SaveAs(self.base_plotdir + '/transitions/plots/' + gene_name +
'.png')