def make_averaged_codon_densities_plot():
experiments = build_all_experiments(verbose=False)
def transform(experiment):
_, concentration = experiment.name.split('_', 1)
concentration, _ = concentration.split('CHX')
if concentration == 'no':
concentration = 0
else:
concentration = concentration.strip('_x')
if '_' in concentration:
num, denom = concentration.split('_')
concentration = float(num) / float(denom)
else:
concentration = int(concentration)
return concentration
sorted_experiments = sorted(experiments['gerashchenko_nar'].values(),
key=transform)
data_sets = [(experiment.name, experiment.read_file('mean_densities'), i)
for i, experiment in enumerate(sorted_experiments)]
visualize.plot_averaged_codon_densities(
data_sets,
'test.pdf',
past_edge=10,
plot_up_to=100,
show_end=True,
)
def make_averaged_codon_densities_plot():
experiments = build_all_experiments(verbose=False)
def transform(experiment):
_, concentration = experiment.name.split('_', 1)
concentration, _ = concentration.split('CHX')
if concentration == 'no':
concentration = 0
else:
concentration = concentration.strip('_x')
if '_' in concentration:
num, denom = concentration.split('_')
concentration = float(num) / float(denom)
else:
concentration = int(concentration)
return concentration
sorted_experiments = sorted(experiments['gerashchenko_nar'].values(), key=transform)
data_sets = [(experiment.name, experiment.read_file('mean_densities'), i)
for i, experiment in enumerate(sorted_experiments)]
visualize.plot_averaged_codon_densities(data_sets,
'test.pdf',
past_edge=10,
plot_up_to=100,
show_end=True,
)
def plot_mean_densities(self):
visualize.plot_averaged_codon_densities([(self.name, self.read_file('mean_densities'), 0)],
self.figure_file_names['mean_densities'],
past_edge=10,
plot_up_to=1000,
smooth=False,
)
def plot_starts_and_ends(self):
short_lengths = range(20, 24)
long_lengths = range(27, 32)
metagene_positions = self.read_file('metagene_positions')
visualize.plot_metagene_positions(metagene_positions,
self.figure_file_names['starts_and_ends'],
long_lengths + ['all', 'all_nonunique'],
title='{0}\n{1}'.format(self.group, self.name),
)
visualize.plot_metagene_positions_rotations(metagene_positions,
self.figure_file_names['starts_and_ends_rotations'],
title='{0}\n{1}'.format(self.group, self.name),
)
visualize.plot_metagene_positions(metagene_positions,
self.figure_file_names['three_prime_starts_and_ends'],
['three_prime_genomic', 'three_prime_nongenomic', 'three_prime_nonunique'],
title='{0}\n{1}'.format(self.group, self.name),
)
visualize.plot_just_ends(metagene_positions['stop_codon'],
self.figure_file_names['ends'],
title='{0}\n{1}'.format(self.group, self.name),
)
visualize.plot_metagene_positions_heatmap(metagene_positions,
self.figure_file_names['starts_and_ends_heatmap'],
#normalize_to_max_in=(range(30, 34), 'start', slice(1, 1000)),
)
visualize.plot_metagene_positions_heatmap(metagene_positions,
self.figure_file_names['starts_and_ends_heatmap_zoomed_out'],
zoomed_out=True,
#normalize_to_max_in=(range(30, 34), 'start', slice(1, 1000)),
)
visualize.plot_averaged_codon_densities([(self.name, self.read_file('mean_densities'), 0)],
self.figure_file_names['mean_densities'],
past_edge=100,
plot_up_to=1000,
)
#visualize.plot_averaged_nucleotide_densities([(self.name, metagene_positions, 0)],
# self.figure_file_names['mean_nucleotide_densities'],
# past_edge=10,
# plot_up_to=2000,
# smooth=False,
# )
visualize.plot_averaged_codon_densities([(self.name, self.read_file('mean_densities_anisomycin'), 0)],
self.figure_file_names['mean_densities_anisomycin'],
past_edge=10,
plot_up_to=500,
)
