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

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")

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")
ValueError: 'color' kwarg must be a color or sequence of color specs. For a sequence of val ...
Traceback (most recent call last): File "/home/docs/.local/share/hatch/env/virtual/hv-anndata/STk7F69l/docs/lib/python3.13/site-packages/matplotlib/axes/_axes.py", line 4692, in _parse_scatter_color_args mcolors.to_rgba_array(kwcolor) ~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^ File "/home/docs/.local/share/hatch/env/virtual/hv-anndata/STk7F69l/docs/lib/python3.13/site-packages/matplotlib/colors.py", line 515, in to_rgba_array rgba = np.array([to_rgba(cc) for cc in c]) ~~~~~~~^^^^ File "/home/docs/.local/share/hatch/env/virtual/hv-anndata/STk7F69l/docs/lib/python3.13/site-packages/matplotlib/colors.py", line 317, in to_rgba rgba = _to_rgba_no_colorcycle(c, alpha) File "/home/docs/.local/share/hatch/env/virtual/hv-anndata/STk7F69l/docs/lib/python3.13/site-packages/matplotlib/colors.py", line 401, in _to_rgba_no_colorcycle raise ValueError(f"Invalid RGBA argument: {orig_c!r}") ValueError: Invalid RGBA argument: np.float64(0.8767174229788279) The above exception was the direct cause of the following exception: Traceback (most recent call last): File "/home/docs/.local/share/hatch/env/virtual/hv-anndata/STk7F69l/docs/lib/python3.13/site-packages/holoviews/plotting/mpl/element.py", line 617, in render_artists handles = self.init_artists(ax, plot_data, plot_kwargs) File "/home/docs/.local/share/hatch/env/virtual/hv-anndata/STk7F69l/docs/lib/python3.13/site-packages/holoviews/plotting/mpl/element.py", line 666, in init_artists artist = plot_fn(*plot_args, **plot_kwargs) File "/home/docs/.local/share/hatch/env/virtual/hv-anndata/STk7F69l/docs/lib/python3.13/site-packages/matplotlib/_api/deprecation.py", line 453, in wrapper return func(*args, **kwargs) File "/home/docs/.local/share/hatch/env/virtual/hv-anndata/STk7F69l/docs/lib/python3.13/site-packages/matplotlib/__init__.py", line 1524, in inner return func( ax, *map(cbook.sanitize_sequence, args), **{k: cbook.sanitize_sequence(v) for k, v in kwargs.items()}) File "/home/docs/.local/share/hatch/env/virtual/hv-anndata/STk7F69l/docs/lib/python3.13/site-packages/matplotlib/axes/_axes.py", line 4954, in scatter self._parse_scatter_color_args( ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ c, edgecolors, kwargs, x.size, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ get_next_color_func=self._get_patches_for_fill.get_next_color) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/docs/.local/share/hatch/env/virtual/hv-anndata/STk7F69l/docs/lib/python3.13/site-packages/matplotlib/axes/_axes.py", line 4694, in _parse_scatter_color_args raise ValueError( ...<2 lines>... "the 'c' argument instead.") from err ValueError: 'color' kwarg must be a color or sequence of color specs. For a sequence of values to be color-mapped, use the 'c' argument instead. 
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']