pyscnet.Plotting

pyscnet.Plotting.geneHeatmap

Created on Thu May 9 11:32:32 2019 @author: mwu

pyscnet.Plotting.geneHeatmap.geneCorrelation(gnetdata, gene, cell_clusterid, select_by, order_by=None, scale_data=True, save_as=None, figsize=None, **kwargs)[source]
Parameters
  • gnetdata – Gnetdata object

  • gene – list, default None.

  • cell_clusterid – str, default None. cell with cell_clusterid will be selected

  • select_by – str, default None. key of filtering cells

  • order_by – str, default None. key of ordering cells

  • scale_data – bool, default True. whether or not scale the data

  • save_as – str, default None. filepath+filename

  • figsize – list, default None. a list of int defining figure size

  • kwargs – additional parameters passed to seaborn.clustermap()

Returns

None

pyscnet.Plotting.geneHeatmap.geneDynamic(gnetdata, gene, cell_clusterid, select_by, rolling=10, order_by=None, scale_data=True, save_as=None, colors=None, legend_size=None, **kwargs)[source]
Parameters
  • gnetdata – Gnetdata object

  • gene – list, default None.

  • cell_clusterid – str, default None. cell with cell_clusterid will be selected

  • select_by – str, default None. key of filtering cells

  • order_by – str, default None. key of ordering cells

  • rolling – int, default 10. rolling window calculation

  • scale_data – bool, default True. whether or not scale the data

  • save_as – str, default None. filepath+filename

  • colors – list, default None. list of string denoting color map

  • legend_size – list, default None. specify legend size

  • kwargs – additional parameters passed to matplotlib.pyplot.plot()

Returns

none

pyscnet.Plotting.geneHeatmap.geneHeatmap(gnetdata, gene, cell_clusterid, select_by, order_by=None, scale_data=True, cmap='RdBu', save_as=None, **kwargs)[source]
Parameters
  • gnetdata – Gnetdata object, default None

  • gene – list, default None.

  • cell_clusterid – str, default None. cell with cell_clusterid will be selected

  • select_by – str, default None. key of filtering cells

  • order_by – str, default None. key of ordering cells

  • scale_data – bool, default True. whether or not scale the data

  • cmap – str, default ‘RdBu’. string denoting colors in clustermap

  • save_as – str, default None. filepath+filename

  • kwargs – additional parameters passed to seaborn.clustermap()

Returns

None

pyscnet.Plotting.show_net

Created on Thu May 9 11:32:32 2019 @author: mwu

pyscnet.Plotting.show_net.dynamic_netShow(gnetdata, filename, node_size=50, html_size=['1200px', '1600px'])[source]
Parameters
  • gnetdata – Gnetdata object

  • filename – str, save as filename

  • node_size – int, default 50.

  • html_size – list, default [“1200px”, “1600px”]

Returns

None

pyscnet.Plotting.show_net.static_netShow(gnetdata, filename, scale=4, figure_size=[20, 10], link_key='consensus', random_path=None, path_highlight=False, neighhours_highlight=False, start=None, **kwargs)[source]
Parameters
  • gnetdata – Gnetdata object

  • filename – str, save as filename

  • scale – int, default 4.

  • figure_size – list, default [20, 10].

  • random_path – list, list of nodes for highlighting.

  • path_highlight – bool, default False.

  • neighhours_highlight – bool, default False.

  • start – str, default None.

  • kwargs – additional parameters passed to networkx.draw_networkx()

Returns

None