hv_anndata.plotting.scanpy.highly_variable_genes

hv_anndata.plotting.scanpy.highly_variable_genes(adata)

Plot dispersions used to identify highly variable genes.

Parameters:
adata AnnData

The AnnData object.

Return type:

Layout

Returns:

A layout containing two Scatter plots, one normalized and one not.

Examples

import scanpy as sc
import hv_anndata.plotting.scanpy as hv_sc
from hv_anndata import data, register, A

register()

adata = data.pbmc68k_processed()
sc.pp.highly_variable_genes(adata)

hv_sc.highly_variable_genes(adata)

/home/docs/.local/share/hatch/env/virtual/hv-anndata/STk7F69l/docs/lib/python3.13/site-packages/numba/cpython/hashing.py:477: UserWarning: FNV hashing is not implemented in Numba. See PEP 456 https://www.python.org/dev/peps/pep-0456/ for rationale over not using FNV. Numba will continue to work, but hashes for built in types will be computed using siphash24. This will permit e.g. dictionaries to continue to behave as expected, however anything relying on the value of the hash opposed to hash as a derived property is likely to not work as expected.
  warnings.warn(msg)

import scanpy as sc
import hv_anndata.plotting.scanpy as hv_sc
from hv_anndata import data, register, A

register()

adata = data.pbmc68k_processed()
sc.pp.highly_variable_genes(adata)

hv_sc.highly_variable_genes(adata)

import scanpy as sc
import hv_anndata.plotting.scanpy as hv_sc
from hv_anndata import data, register, A

register()

adata = data.pbmc68k_processed()
sc.pp.highly_variable_genes(adata)

hv_sc.highly_variable_genes(adata)

WARNING:param.main: Option 'legend_labels' for Scatter type not valid for selected backend ('plotly'). Option only applies to following backends: ['bokeh', 'matplotlib']
WARNING:param.main: Option 'legend_position' for Scatter type not valid for selected backend ('plotly'). Option only applies to following backends: ['bokeh', 'matplotlib']
WARNING:param.main: Option 'legend_labels' for Scatter type not valid for selected backend ('plotly'). Option only applies to following backends: ['bokeh', 'matplotlib']
WARNING:param.main: Option 'legend_position' for Scatter type not valid for selected backend ('plotly'). Option only applies to following backends: ['bokeh', 'matplotlib']