hv_anndata.plotting.scanpy.ranking¶

hv_anndata.plotting.scanpy.ranking(adata, ref, /, n_points=10, *, include_lowest=True, label_dim=None)¶

Plot (e.g. PCA) score ranking.

Parameters:

adata AnnData: Annotated data matrix.
ref AdDim: Dimension containing scores to rank.
n_points int, default: 10: Number of points to plot.
include_lowest bool, default: True: Whether to include the lowest-scored names in addition to the highest-scored ones.
label_dim AdDim | None, default: None: Dimension to use for labels. The default is dim’s axis index (e.g. A.obs.index for A.obs["scores"]).

Return type:

Labels

Returns:

Holoviews plot with labels and points.

Examples

bokeh

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

register()

adata = data.pbmc68k_processed()
hv.Layout([
    hv_sc.ranking(adata, A.varm["PCs"][0]).opts(aspect=1.2),
    hv_sc.ranking(adata, A.varm["PCs"][0], include_lowest=False).opts(aspect=0.6),
]).opts(shared_axes=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.Layout([
    hv_sc.ranking(adata, A.varm["PCs"][0]).opts(aspect=1.2),
    hv_sc.ranking(adata, A.varm["PCs"][0], include_lowest=False).opts(aspect=0.6),
]).opts(shared_axes=False)

WARNING:param.main: Option 'angle' for Labels type not valid for selected backend ('matplotlib'). Option only applies to following backends: ['bokeh']
WARNING:param.main: Option 'text_align' for Labels type not valid for selected backend ('matplotlib'). Option only applies to following backends: ['bokeh']
WARNING:param.main: Option 'angle' for Labels type not valid for selected backend ('matplotlib'). Option only applies to following backends: ['bokeh']
WARNING:param.main: Option 'text_align' for Labels type not valid for selected backend ('matplotlib'). Option only applies to following backends: ['bokeh']

plotly

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

register()

adata = data.pbmc68k_processed()
hv.Layout([
    hv_sc.ranking(adata, A.varm["PCs"][0]).opts(aspect=1.2),
    hv_sc.ranking(adata, A.varm["PCs"][0], include_lowest=False).opts(aspect=0.6),
]).opts(shared_axes=False)

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