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, )