pegasus.plot_gsea

pegasus.plot_gsea(data, gsea_keyword, alpha=0.1, top_n=20, panel_size=(6, 4), return_fig=False, dpi=300.0, **kwargs)[source]

Generate GSEA barplots

Parameters

  • data (UnimodalData or MultimodalData object) – The main data object.

  • gsea_keyword (str) – Keyword in data.uns that stores the fGSEA results in pandas data frame.

  • alpha (float, optional, default: 0.1) – False discovery rate threshold.

  • top_n (int, optional, default: 20) – Only show top_n up/down regulated pathways.

  • panel_size (tuple, optional (default: (6, 4))) – The plot size (width, height) in inches.

  • return_fig (bool, optional, default: False) – Return a Figure object if True; return None otherwise.

  • dpi (float, optional, default: 300.0) – The resolution in dots per inch.

Returns

A matplotlib.figure.Figure object containing the dot plot if return_fig == True. Each figure contains two panels. The top panel shows up-regulated pathways (color: red) and the bottom panel shows down-regulated pathways (color: green).

Return type

Figure object

Examples

>>> fig = pg.plot_gsea(data, 'fgsea_out', dpi = 500)