Examples

Sample data

Open Cytoscape and select the Yeast Perturbation sample data.

Click File > Export > Network to File... to export it as an XGMML format file.

The exported yeast_perturbation.xgmml file is stored in this directory of the repository.

Reader

Run the following code to read the XGMML file with NetworkxXGMMLReader:

from xgmml.reader.networkx_xgmml_reader import NetworkxXGMMLReader

xgmml_reader = NetworkxXGMMLReader()
yeast_perturbation_graph = xgmml_reader.read('yeast_perturbation.xgmml')

Run the following code to view the basic information of the graph:

yeast_perturbation_graph.is_directed()
# True

len(yeast_perturbation_graph.nodes)
# 330

len(yeast_perturbation_graph.edges)
# 359

Writer

Run the following code to write the graph into an XGMML file with NetworkxXGMMLWriter:

from xgmml.writer.networkx_xgmml_writer import NetworkxXGMMLWriter

xgmml_writer = NetworkxXGMMLWriter()
xgmml_writer.write(
    yeast_perturbation_graph,
    'yeast_perturbation.xgmml',
    graph_label='Yeast Perturbation (Default)',
)

Import it into Cytoscape. The visualization is shown as below:

Run the following code to create a similar style to the original XGMML file and write it into an XGMML file:

import matplotlib as mpl
from xgmml.writer.networkx_xgmml_writer import NetworkxXGMMLWriter
from xgmml.style.style_mapper import *

class StyleNodeSizeMapper(StyleNodeSizeDefaultContinuousMapper):
    def __init__(self, values, **kwargs):
        super(StyleNodeSizeMapper, self).__init__(values, **kwargs)

        self._min_size = 40
        self._max_size = 150


class StyleNodeLabelFontSizeMapper(StyleFontSizeDefaultContinuousMapper):
    def __init__(self, values, **kwargs):
        super(StyleNodeLabelFontSizeMapper, self).__init__(values, **kwargs)

        self._min_size = 10
        self._max_size = 40


class StyleNodeFillColorMapper(StyleColorContinuousMapper):
    def __init__(self, values, **kwargs):
        colors = ['#0066CC', '#FFFFFF', '#FFFF00']
        colormap = mpl.colors.LinearSegmentedColormap.from_list('custom', colors)

        super(StyleNodeFillColorMapper, self).__init__(
            values, colormap=colormap, **kwargs
        )

xgmml_writer = NetworkxXGMMLWriter()
xgmml_writer.write(
    yeast_perturbation_graph,
    'yeast_perturbation.xgmml',
    graph_label='Yeast Perturbation (Restore Style)',
    node_label_key='COMMON',
    node_width_key='degree.layout',
    node_width_mapper=StyleNodeSizeMapper,
    node_height_key='degree.layout',
    node_height_mapper=StyleNodeSizeMapper,
    node_label_font_size_key='Degree',
    node_label_font_size_mapper=StyleNodeLabelFontSizeMapper,
    node_fill_color_key='gal1RGexp',
    node_fill_color_mapper=StyleNodeFillColorMapper,
)

Import it into Cytoscape. The visualization is show as below:

Click Layout > Prefuse Force Directed Layout to get a better layout.