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/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(