Ctrl+K

scgenome.pl.plot_cn_profile

scgenome.pl.plot_cn_profile#

scgenome.pl.plot_cn_profile(adata, obs_id, value_layer_name=None, state_layer_name=None, ax=None, palette=None, chromosome=None, start=None, end=None, squashy=False, tick_major_spacing=None, tick_minor_spacing=None, **kwargs)#

Plot scatter points of copy number across the genome or a chromosome.

Parameters:

  • adata (AnnData) – copy number data

  • obs_id (str) – observation to plot

  • value_layer_name (str, optional) – layer with values for y axis, None for X, by default None

  • state_layer_name (str, optional) – layer with states for colors, None for no color by state, by default None

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

  • palette (str, optional) – color palette passed to sns.scatterplot

  • chromosome (str, optional) – single chromosome plot, by default None

  • start (int, optional) – start of plotting region

  • end (int, optional) – end of plotting region

  • squashy (bool, optional) – compress y axis, by default False

  • rawy (bool, optional) – raw data on y axis, by default False

  • tick_major_spacing (int, optional) – major tick spacing, by default

  • tick_minor_spacing (int, optional) – minor tick spacing, by default 1e6

  • **kwargs – kwargs for sns.scatterplot

Returns:

Axes used for plotting

Return type:

matplotlib.axes.Axes

Examples

import scgenome
adata = scgenome.datasets.OV2295_HMMCopy_reduced()
scgenome.pl.plot_cn_profile(adata, 'SA922-A90554B-R27-C43', value_layer_name='copy', state_layer_name='state')
../_images/scgenome-pl-plot_cn_profile-1.png