scgenome.pl.plot_cell_cn_matrix

scgenome.pl.plot_cell_cn_matrix(adata, layer_name='state', cell_order_fields=(), ax=None, raw=False, max_cn=13, vmin=None, vmax=None, cmap=None, show_cell_ids=False)

Plot a copy number matrix

Parameters:

• adata (AnnData) – copy number data

• layer_name (str, optional) – layer with copy number data to plot, None for X, by default ‘state’

• cell_order_fields (list, optional) – columns of obs on which to sort cells, by default None

• ax (matplotlib.axes.Axes, optional) – existing axis to plot into, by default None

• raw (bool, optional) – raw plotting, no integer color map, by default False

• max_cn (int, optional) – clip cn at max value, raw=False only, by default 13

• vmin (float, optional) – for raw=True, vmin and vmax define the data range that the colormap covers, see matplotlib.pyplot.imshow

• vmax (float, optional) – for raw=True, vmin and vmax define the data range that the colormap covers, see matplotlib.pyplot.imshow

• cmap (str, optional) – matplotlib colormap name, only used if raw=True

• show_cell_ids (bool, optional) – show cell ids on heatmap axis, by default False

Returns:

Dictionary of plot and data elements

Return type:

dict

Examples

import scgenome
adata = scgenome.datasets.OV2295_HMMCopy_reduced()
scgenome.pl.plot_cell_cn_matrix(adata)