decoupler.plot_filter_by_expr
- decoupler.plot_filter_by_expr(adata, obs=None, group=None, lib_size=None, min_count=10, min_total_count=15, large_n=10, min_prop=0.7, cmap='viridis', figsize=(5, 4), dpi=100, ax=None, return_fig=False, save=None, **kwargs)
Plot to help determining the thresholds of the
decoupler.filter_by_exprfunction.- Parameters:
- adataAnnData
AnnData obtained after running
decoupler.get_pseudobulk.- obsDataFrame, None
If provided, metadata dataframe, only needed if
adatais not anAnnData.- groupstr, None
Name of the
.obscolumn to group by. If None, it assumes that all samples belong to one group.- lib_sizeint, float, None
Library size. If None, default to the sum of reads per sample.
- min_countint
Minimum count requiered per gene for at least some samples.
- min_total_countint
Minimum total count required per gene across all samples.
- large_nint
Number of samples per group that is considered to be “large”.
- min_propfloat
Minimum proportion of samples in the smallest group that express the gene.
- cmapstr
Colormap to use.
- figsizetuple
Figure size.
- dpiint
DPI resolution of figure.
- axAxes, None
A matplotlib axes object. If None returns new figure.
- return_figbool
Whether to return a Figure object or not.
- savestr, None
Path to where to save the plot. Infer the filetype if ending on {
.pdf,.png,.svg}.- kwargsdict
Other keyword arguments are passed through to
sns.histplot.
- Returns:
- figFigure, None
If return_fig, returns Figure object.