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
orMultimodalData
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 aFigure
object ifTrue
; returnNone
otherwise.dpi (
float
, optional, default:300.0
) – The resolution in dots per inch.
- Returns
A
matplotlib.figure.Figure
object containing the dot plot ifreturn_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)