hv_anndata.plotting.scanpy.embedding_density¶

hv_anndata.plotting.scanpy.embedding_density(adata, basis, *, groupby=None, key=None)¶

Plot embedding density.

Parameters:

adata AnnData: Annotated data matrix.
basis MultiAcc: Embedding to plot (e.g. A.obsm["X_umap"]).
groupby str | None, default: None: groupby as specified in scanpy.tl.embedding_density().
key str | None, default: None: key_added as specified in scanpy.tl.embedding_density().

Return type:

Scatter | NdLayout

Returns:

Scatter plot if groupby is None, else a layout of scatter plots.

Examples

bokeh

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.tl.embedding_density(adata, basis="umap", groupby="phase")
hv_sc.embedding_density(adata, A.obsm["X_umap"], groupby="phase")

/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)

matplotlib

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.tl.embedding_density(adata, basis="umap", groupby="phase")
hv_sc.embedding_density(adata, A.obsm["X_umap"], groupby="phase")

plotly

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.tl.embedding_density(adata, basis="umap", groupby="phase")
hv_sc.embedding_density(adata, A.obsm["X_umap"], groupby="phase")

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