def plot_starts_and_ends(self):
metagene_positions = self.read_file('metagene_positions')
visualize.plot_metagene_positions(metagene_positions,
self.figure_file_names['starts_and_ends'],
['five_prime', 'three_prime_genomic', 'three_prime_nongenomic'],
)
def plot_starts_and_ends(self):
metagene_positions = self.read_file('metagene_positions')
visualize.plot_metagene_positions(metagene_positions,
self.figure_file_names['starts_and_ends'],
['all'],
)
def plot_starts_and_ends(self):
metagene_positions = self.read_file('metagene_positions')
visualize.plot_metagene_positions(
metagene_positions,
self.figure_file_names['starts_and_ends'],
['all'],
)
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,
)
