hv_anndata.plotting.scanpy.violin¶

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

Overloads:

adata (AnnData), vdims (AdDim), kdims (Collection[AdDim]), color (AdDim | None) → hv.Violin
adata (AnnData), vdims (Collection[AdDim]), kdims (Collection[AdDim]), color (AdDim | None) → hv.Layout

Shortcut for a violin plot.

If vdims is an AdDim, a single violin is returned:

>>> hv.Violin(adata, kdims, [vdims, color]).opts(violin_fill_color=color, ...)

Otherwise, a layout is returned:

>>> hv.Layout([violin(adata, kdims, vdim, ...) for vdim in vdims]).opts(...)

Parameters:

adata AnnData: The AnnData object.
vdims Collection[AdDim] | AdDim: The value dimension(s). If multiple, a Layout is returned.
kdims Collection[AdDim], default: (): The key dimensions (color will be added automatically).
color AdDim | None, default: None: The color dimension.

Returns:

if isinstance(vdims, AdDim):: A Violin plot.
else:: A Layout containing Violin plots.

Examples

bokeh

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

register()

adata = data.pbmc68k_processed()
hv_sc.violin(adata, A.obs[["percent_mito", "n_counts", "n_genes"]]).opts(
    hv.opts.Violin(ylim=(0, None))
)

/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.violin(adata, A.obs[["percent_mito", "n_counts", "n_genes"]]).opts(
    hv.opts.Violin(ylim=(0, None))
)

plotly

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

register()

adata = data.pbmc68k_processed()
hv_sc.violin(adata, A.obs[["percent_mito", "n_counts", "n_genes"]]).opts(
    hv.opts.Violin(ylim=(0, None))
)

bokeh

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

register()

adata = data.pbmc68k_processed()
hv_sc.violin(adata, A.obs["S_score"], color=A.obs["bulk_labels"]).opts(
    width=500, xrotation=30
)

matplotlib

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

register()

adata = data.pbmc68k_processed()
hv_sc.violin(adata, A.obs["S_score"], color=A.obs["bulk_labels"]).opts(
    width=500, xrotation=30
)

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

plotly

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

register()

adata = data.pbmc68k_processed()
hv_sc.violin(adata, A.obs["S_score"], color=A.obs["bulk_labels"]).opts(
    width=500, xrotation=30
)

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