Source code for pybel_tools.summary.export

# -*- coding: utf-8 -*-

"""Functions for summarizing graphs.

This module contains functions that provide aggregate summaries of graphs including visualization with matplotlib,
printing summary information, and exporting summarized graphs
"""

from __future__ import print_function

import logging
import warnings

import pandas as pd

from pybel.struct.summary.node_summary import count_functions
from .edge_summary import count_relations

__all__ = [
    'plot_summary_axes',
    'plot_summary',
    'info_list',
    'info_str',
    'info_json',
    'print_summary',
]

log = logging.getLogger(__name__)



[docs]def plot_summary_axes(graph, lax, rax, logx=True):
    """Plots your graph summary statistics on the given axes.

    After, you should run :func:`plt.tight_layout` and you must run :func:`plt.show` to view.

    Shows:
    1. Count of nodes, grouped by function type
    2. Count of edges, grouped by relation type

    :param pybel.BELGraph graph: A BEL graph
    :param lax: An axis object from matplotlib
    :param rax: An axis object from matplotlib

    Example usage:

    >>> import matplotlib.pyplot as plt
    >>> from pybel import from_pickle
    >>> from pybel_tools.summary import plot_summary_axes
    >>> graph = from_pickle('~/dev/bms/aetionomy/parkinsons.gpickle')
    >>> fig, axes = plt.subplots(1, 2, figsize=(10, 4))
    >>> plot_summary_axes(graph, axes[0], axes[1])
    >>> plt.tight_layout()
    >>> plt.show()
    """
    ntc = count_functions(graph)
    etc = count_relations(graph)

    df = pd.DataFrame.from_dict(dict(ntc), orient='index')
    df_ec = pd.DataFrame.from_dict(dict(etc), orient='index')

    df.sort_values(0, ascending=True).plot(kind='barh', logx=logx, ax=lax)
    lax.set_title('Number of nodes: {}'.format(graph.number_of_nodes()))

    df_ec.sort_values(0, ascending=True).plot(kind='barh', logx=logx, ax=rax)
    rax.set_title('Number of edges: {}'.format(graph.number_of_edges()))




[docs]def plot_summary(graph, plt, logx=True, **kwargs):
    """Plots your graph summary statistics. This function is a thin wrapper around :func:`plot_summary_axis`. It
    automatically takes care of building figures given matplotlib's pyplot module as an argument. After, you need
    to run :func:`plt.show`.

    :code:`plt` is given as an argument to avoid needing matplotlib as a dependency for this function

    Shows:

    1. Count of nodes, grouped by function type
    2. Count of edges, grouped by relation type

    :param pybel.BELGraph graph: A BEL graph
    :param plt: Give :code:`matplotlib.pyplot` to this parameter
    :param kwargs: keyword arguments to give to :func:`plt.subplots`

    Example usage:

    >>> import matplotlib.pyplot as plt
    >>> from pybel import from_pickle
    >>> from pybel_tools.summary import plot_summary
    >>> graph = from_pickle('~/dev/bms/aetionomy/parkinsons.gpickle')
    >>> plot_summary(graph, plt, figsize=(10, 4))
    >>> plt.show()
    """
    fig, axes = plt.subplots(1, 2, **kwargs)
    lax = axes[0]
    rax = axes[1]

    plot_summary_axes(graph, lax, rax, logx=logx)
    plt.tight_layout()

    return fig, axes




[docs]def info_list(graph):
    """Returns useful information about the graph as a list of tuples

    :param pybel.BELGraph graph: A BEL graph
    :rtype: list
    """
    warnings.warn('info_list is deprecated.', DeprecationWarning)
    return graph._describe_list()




[docs]def info_json(graph):
    """Returns useful information about the graph as a dictionary

    :param pybel.BELGraph graph: A BEL graph
    :rtype: dict
    """
    warnings.warn('info_json is deprecated. Use BELGraph.summary_dict()', DeprecationWarning)
    return graph.summary_dict()




[docs]def info_str(graph):
    """Puts useful information about the graph in a string

    :param pybel.BELGraph graph: A BEL graph
    :rtype: str
    """
    warnings.warn('info_str is deprecaged. Use BELGraph.summary_str()', DeprecationWarning)
    return graph.summary_str()