pegasus.plot_gsea

pegasus.plot_gsea(data, gsea_keyword='gsea_out', alpha=0.1, top_n=20, panel_size=(6, 4), label_fontsize=5, return_fig=False, dpi=300.0, **kwargs)[source]

Generate GSEA barplots

Parameters

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

  • gsea_keyword (str, optional, default: gsea_out) – Keyword in data.uns that stores the GSEA 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.

  • label_fontsize (int, optional, default: 5) – The font size of labels.

  • 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.

Return type

Optional[Figure]

Returns

  • Figure object – 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).

Examples

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