decoupler.pl.network

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decoupler.pl.network#

decoupler.pl.network(net, data=None, score=None, sources=5, targets=10, by_abs=True, size_node=5, size_label=2.5, s_cmap='RdBu_r', t_cmap='viridis', vcenter=False, c_pos_w='darkgreen', c_neg_w='darkred', s_label='Enrichment\\nscore', t_label='Gene\\nexpression', layout='kk', kw_igraph=None, **kwargs)#

Plot results of enrichment analysis as network.

Parameters:

  • net – Dataframe in long format. Must include source and target columns, and optionally a weight column.

  • data (DataFrame (default: None)) – Input of enrichment analysis, needs to be a one row dataframe with targets as features. Used to filter net.

  • score (DataFrame (default: None)) – Ouput of enrichment analysis, needs to be a one row dataframe with sources as features. Used to filter net.

  • sources (int | list | str (default: 5)) – Number of top sources to plot or list of source names.

  • targets (int | list | str (default: 10)) – Number of top targets to plot or list of target names.

  • by_abs (bool (default: True)) – Whether to consider the absolute value when sorting for n_sources and n_targets.

  • size_node (int (default: 5)) – Size of the nodes in the plot.

  • size_label (float | int (default: 2.5)) – Size of the labels in the plot.

  • s_cmap (str (default: 'RdBu_r')) – Color or colormap to use to color sources.

  • t_cmap (str (default: 'viridis')) – Color or colormap to use to color targets.

  • vcenter (bool (default: False)) – Whether to center colors around 0.

  • c_pos_w (str (default: 'darkgreen')) – Color for edges with positive weights. If no weights are available, they are set to positive by default.

  • c_neg_w (str (default: 'darkred')) – Color for edges with negative weights.

  • s_label (str (default: 'Enrichment\\nscore')) – Label to place in the source colorbar.

  • t_label (str (default: 'Gene\\nexpression')) – Label to place in the target colorbar.

  • layout (str (default: 'kk')) – Layout to use to order the nodes. Check igraph documentation for more options.

  • kw_igraph (dict | None (default: None)) – Keyword arguments passed to igraph.plot.

  • ax – An existing matplotlib.axes._axes.Axes instance to plot on. If None, a new figure and axes will be created.

  • figsize – Size of the figure in inches as (width, height).

  • dpi – Dots per inch for the figure resolution.

  • return_fig – If True, plotting methods should return the figure object instead of showing it.

  • save – If set, path to save the plot automatically to a file.

Returns:

If return_fig=True, returns matplotlib.figure.Figure instance.

Example

import decoupler as dc

adata, net = dc.ds.toy()
dc.pl.network(net, figsize=(4, 4))
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