<filename>python/plot_lsa_entropies_exact_single.py<gh_stars>0
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Author: <NAME> and <NAME>
import os
import sys

import matplotlib
matplotlib.use('Agg')
from matplotlib import pyplot as plt
import numpy as np
from pandas import DataFrame
import scipy.stats
import seaborn as sns

import lsa
from plot_helpers import make_entity_from_fields
from plot_helpers import validate_fname

N_FREQS_LIST = [2**x for x in range(15)]

def gather_entropies_for_seq_file(
        output_dir_name,
        seq_file_name):
    # Where we store outputs
    entropy_dict = {}
    entropy_repeated_dict = {}
    entropy_unrepeated_dict = {}

    # Filtering files based on seq file
    seq_file_prefix = seq_file_name[:-4]
    for fname in os.listdir(output_dir_name):
        fields = validate_fname(fname, 'lsa.w.txt', file_prefix=seq_file_prefix, n_freqs_list=N_FREQS_LIST)
        if fields is None:
            continue
        topic_ct = fields['topic_ct']

        # Compute average entropies
        repeats_mask, w_matrix = lsa.read_in_w(os.path.join(output_dir_name, fname))
        entropies = lsa.compute_entropies(w_matrix)
        entropy_dict[topic_ct] = np.mean(entropies)
        entropy_repeated_dict[topic_ct] = np.mean(entropies[repeats_mask])
        entropy_unrepeated_dict[topic_ct] = np.mean(entropies[np.logical_not(repeats_mask)])

    return (entropy_dict, entropy_repeated_dict, entropy_unrepeated_dict)


def plot_exact_entropies(
        input_dir_name,
        output_dir_name,
        file_prefix,
        save_file,
        process=None):
    entropies = []

    for seq_fname in os.listdir(input_dir_name):
        # Check sequence filename is valid
        seq_fields = validate_fname(seq_fname, 'txt', file_prefix=file_prefix, process=process, n_freqs_list=N_FREQS_LIST)
        if seq_fields is None:
            continue

        entropy_dict, entropy_duplicated, entropy_singular = gather_entropies_for_seq_file(
            output_dir_name,
            seq_fname)
        entropies += [make_entity_from_fields(
                n_topics, ent, 'all', seq_fields
            ) for n_topics, ent in entropy_dict.items()]
        entropies += [make_entity_from_fields(
                n_topics, ent, 'duplicated', seq_fields
            ) for n_topics, ent in entropy_duplicated.items()]
        entropies += [make_entity_from_fields(
                n_topics, ent, 'unduplicated', seq_fields
            ) for n_topics, ent in entropy_singular.items()]


    plt.figure(figsize=(50, 30))
    dataf = DataFrame([e for e in entropies])
    sns.set(font_scale=1.5)
    g = sns.FacetGrid(
            dataf,
            col='n_topics',
            row='label',
            legend_out='true')
    g.map(sns.pointplot, 'frequency', 'entropy')
    g.set_titles(col_template="{col_name} topics", row_template="{row_name}")
    g.set_axis_labels("# copies", "Entropy")
    g.set_xticklabels(rotation=90)
    #g.fig.subplots_adjust(right=.9)
    plt.savefig(save_file)


if __name__ == '__main__':
    in_dir = sys.argv[1]
    out_dir = sys.argv[2]
    file_prefix = sys.argv[3]
    save_file = sys.argv[4]
    plot_exact_entropies(in_dir, out_dir, file_prefix, save_file)


<filename>python/plot_lsa_entropies_exact_single.py<gh_stars>0
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Author: <NAME> and <NAME>
import os
import sys

import matplotlib
matplotlib.use('Agg')
from matplotlib import pyplot as plt
import numpy as np
from pandas import DataFrame
import scipy.stats
import seaborn as sns

import lsa
from plot_helpers import make_entity_from_fields
from plot_helpers import validate_fname

N_FREQS_LIST = [2**x for x in range(15)]

def gather_entropies_for_seq_file(
        output_dir_name,
        seq_file_name):
    # Where we store outputs
    entropy_dict = {}
    entropy_repeated_dict = {}
    entropy_unrepeated_dict = {}

    # Filtering files based on seq file
    seq_file_prefix = seq_file_name[:-4]
    for fname in os.listdir(output_dir_name):
        fields = validate_fname(fname, 'lsa.w.txt', file_prefix=seq_file_prefix, n_freqs_list=N_FREQS_LIST)
        if fields is None:
            continue
        topic_ct = fields['topic_ct']

        # Compute average entropies
        repeats_mask, w_matrix = lsa.read_in_w(os.path.join(output_dir_name, fname))
        entropies = lsa.compute_entropies(w_matrix)
        entropy_dict[topic_ct] = np.mean(entropies)
        entropy_repeated_dict[topic_ct] = np.mean(entropies[repeats_mask])
        entropy_unrepeated_dict[topic_ct] = np.mean(entropies[np.logical_not(repeats_mask)])

    return (entropy_dict, entropy_repeated_dict, entropy_unrepeated_dict)


def plot_exact_entropies(
        input_dir_name,
        output_dir_name,
        file_prefix,
        save_file,
        process=None):
    entropies = []

    for seq_fname in os.listdir(input_dir_name):
        # Check sequence filename is valid
        seq_fields = validate_fname(seq_fname, 'txt', file_prefix=file_prefix, process=process, n_freqs_list=N_FREQS_LIST)
        if seq_fields is None:
            continue

        entropy_dict, entropy_duplicated, entropy_singular = gather_entropies_for_seq_file(
            output_dir_name,
            seq_fname)
        entropies += [make_entity_from_fields(
                n_topics, ent, 'all', seq_fields
            ) for n_topics, ent in entropy_dict.items()]
        entropies += [make_entity_from_fields(
                n_topics, ent, 'duplicated', seq_fields
            ) for n_topics, ent in entropy_duplicated.items()]
        entropies += [make_entity_from_fields(
                n_topics, ent, 'unduplicated', seq_fields
            ) for n_topics, ent in entropy_singular.items()]


    plt.figure(figsize=(50, 30))
    dataf = DataFrame([e for e in entropies])
    sns.set(font_scale=1.5)
    g = sns.FacetGrid(
            dataf,
            col='n_topics',
            row='label',
            legend_out='true')
    g.map(sns.pointplot, 'frequency', 'entropy')
    g.set_titles(col_template="{col_name} topics", row_template="{row_name}")
    g.set_axis_labels("# copies", "Entropy")
    g.set_xticklabels(rotation=90)
    #g.fig.subplots_adjust(right=.9)
    plt.savefig(save_file)


if __name__ == '__main__':
    in_dir = sys.argv[1]
    out_dir = sys.argv[2]
    file_prefix = sys.argv[3]
    save_file = sys.argv[4]
    plot_exact_entropies(in_dir, out_dir, file_prefix, save_file)


#!/usr/bin/env python # -*- coding: utf-8 -*- # Author: <NAME> and <NAME> # Where we store outputs # Filtering files based on seq file # Compute average entropies # Check sequence filename is valid #g.fig.subplots_adjust(right=.9)