hv_anndata.plotting.scanpy.scatter¶

hv_anndata.plotting.scanpy.scatter(adata, /, kdims, vdims=(), *, color=None)¶

Shortcut for a scatter plot.

Basically just

>>> hv.Scatter(adata, kdims[0], [kdims[1], *vdims]).opts(aspect="square", ...)

If color is set, it’s both added to vdims and in .opts(color=...).

Parameters:

adata AnnData: The AnnData object.
kdims Collection[AdDim]: A sequence containing the x and y dimension.
vdims Collection[AdDim], default: (): The value dimensions (color will be added automatically).
color AdDim | None, default: None: The color dimension.

Return type:

Scatter

Returns:

A scatter plot object

Examples

bokeh

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

register()

adata = data.pbmc68k_processed()
hv_sc.scatter(adata, A.X[:, ["PSAP", "C1QA"]], color=A.obs["bulk_labels"]).opts(
    cmap="tab10", show_legend=False
)

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

register()

adata = data.pbmc68k_processed()
hv_sc.scatter(adata, A.X[:, ["PSAP", "C1QA"]], color=A.obs["bulk_labels"]).opts(
    cmap="tab10", show_legend=False
)

plotly

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

register()

adata = data.pbmc68k_processed()
hv_sc.scatter(adata, A.X[:, ["PSAP", "C1QA"]], color=A.obs["bulk_labels"]).opts(
    cmap="tab10", show_legend=False
)

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