hv_anndata.plotting.utils.highest_expr_genes

hv_anndata.plotting.utils.highest_expr_genes(adata, n_top=20, *, layer=None, gene_symbols=None)

Get n_top genes by mean expression.

Used in hv_anndata.plotting.scanpy.highest_expr_genes().

Parameters:
adata AnnData

The AnnData object.

n_top int, default: 20

The number of top genes to return.

layer str | None, default: None

The layer to use.

gene_symbols str | None, default: None

The .var column name containing gene symbols.

Return type:

AnnData

Returns:

A AnnData object containing normalized expressions for the top n_top genes.

Examples

from hv_anndata import data, register, A
from hv_anndata.plotting import utils as hv_sc_utils

register()

adata = data.pbmc68k_processed()
adata_hi_expr = hv_sc_utils.highest_expr_genes(adata)
hv.HeatMap(adata_hi_expr, [A.obs.index, A.var.index], A.X[:, :]).opts(
    xrotation=30
)

/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)

/home/docs/checkouts/readthedocs.org/user_builds/hv-anndata/checkouts/latest/src/hv_anndata/plotting/utils.py:55: UserWarning: Some cells have zero counts
  norm_expr = sc.pp.normalize_total(

from hv_anndata import data, register, A
from hv_anndata.plotting import utils as hv_sc_utils

register()

adata = data.pbmc68k_processed()
adata_hi_expr = hv_sc_utils.highest_expr_genes(adata)
hv.HeatMap(adata_hi_expr, [A.obs.index, A.var.index], A.X[:, :]).opts(
    xrotation=30
)

/home/docs/checkouts/readthedocs.org/user_builds/hv-anndata/checkouts/latest/src/hv_anndata/plotting/utils.py:55: UserWarning: Some cells have zero counts
  norm_expr = sc.pp.normalize_total(

from hv_anndata import data, register, A
from hv_anndata.plotting import utils as hv_sc_utils

register()

adata = data.pbmc68k_processed()
adata_hi_expr = hv_sc_utils.highest_expr_genes(adata)
hv.HeatMap(adata_hi_expr, [A.obs.index, A.var.index], A.X[:, :]).opts(
    xrotation=30
)

/home/docs/checkouts/readthedocs.org/user_builds/hv-anndata/checkouts/latest/src/hv_anndata/plotting/utils.py:55: UserWarning: Some cells have zero counts
  norm_expr = sc.pp.normalize_total(