infercnvpy.pl.chromosome_heatmap

infercnvpy.pl.chromosome_heatmap(adata, *, groupby='cnv_leiden', use_rep='cnv', cmap='bwr', figsize=(16, 10), show=None, save=None, **kwargs)

Plot a heatmap of smoothed gene expression by chromosome.

Wrapper around scanpy.pl.heatmap().

Parameters

adata : AnnData

annotated data matrix

groupby : str (default: 'cnv_leiden')

group the cells by a categorical variable from adata.obs. It usually makes sense to either group by unsupervised clustering obtained from infercnvpy.tl.leiden() (the default) or a cell-type label.

use_rep : str (default: 'cnv')

Key under which the result from infercnvpy.tl.infercnv() are stored.

cmap : str | ColormapUnion[str, Colormap] (default: 'bwr')

colormap to use

figsize : Tuple[int, int] (default: (16, 10))

(width, height) tuple in inches

show : bool | NoneOptional[bool] (default: None)

Whether to show the figure or to return the axes objects.

save : str | bool | NoneUnion[str, bool, None] (default: None)

If True or a str, save the figure. A string is appended to the default filename. Infer the filetype if ending on {'.pdf', '.png', '.svg'}.

**kwargs

Arguments passed on to scanpy.pl.heatmap().

Return type

{str: Axes} | NoneOptional[Dict[str, Axes]]

Returns

If show is False, a dictionary of axes.