Visualizing pre-processing results

%load_ext autoreload
%autoreload 2

import holoviews as hv

from hv_anndata import A, register
from hv_anndata import scanpy as hv_sc
from hv_anndata.plotting import utils as hv_sc_utils

register()

hv.extension("bokeh")

ⓘ

import scanpy as sc

adata = sc.datasets.pbmc68k_reduced()
adata.layers["counts"] = adata.raw.X
del adata.raw
adata

AnnData object with n_obs × n_vars = 700 × 765
    obs: 'bulk_labels', 'n_genes', 'percent_mito', 'n_counts', 'S_score', 'G2M_score', 'phase', 'louvain'
    var: 'n_counts', 'means', 'dispersions', 'dispersions_norm', 'highly_variable'
    uns: 'bulk_labels_colors', 'louvain', 'louvain_colors', 'neighbors', 'pca', 'rank_genes_groups'
    obsm: 'X_pca', 'X_umap'
    varm: 'PCs'
    obsp: 'connectivities', 'distances'
    layers: None, 'counts'

scanpy.pl.highest_expr_genes()

tool to get the data:

hv.HeatMap(
    hv_sc_utils.highest_expr_genes(adata), [A.obs.index, A.var.index], A.X[:, :]
).opts(responsive=True, height=400, 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(

plotting function using above data

hv_sc.highest_expr_genes(adata, layer="counts")

scanpy.pl.highly_variable_genes()

sc.pp.highly_variable_genes(adata)
# sc.pl.highly_variable_genes(adata)

hv_sc.highly_variable_genes(adata)

scanpy.pl.scrublet_score_distribution()

TODO:

• batches

missing:

• where are the y ticks on the y axis?

adata_sim = sc.pp.scrublet_simulate_doublets(adata)
sc.pp.scrublet(adata, adata_sim)
# sc.pl.scrublet_score_distribution(adata)

hv_sc.scrublet_score_distribution(adata)

/home/docs/.local/share/hatch/env/virtual/hv-anndata/STk7F69l/docs/lib/python3.13/site-packages/holoviews/core/dimension.py:1073: FutureWarning: Probably comparing to a dimension created from `Dimension.name`. This will not be supported in the future, please report as an issue. 
  return next(i for i, d in enumerate(dimensions) if d == dim)
/home/docs/.local/share/hatch/env/virtual/hv-anndata/STk7F69l/docs/lib/python3.13/site-packages/holoviews/core/data/grid.py:326: FutureWarning: Probably comparing to a dimension created from `Dimension.name`. This will not be supported in the future, please report as an issue. 
  if d not in dataset.kdims+virtual_coords]
/home/docs/.local/share/hatch/env/virtual/hv-anndata/STk7F69l/docs/lib/python3.13/site-packages/holoviews/core/dimension.py:1073: FutureWarning: Probably comparing to a dimension created from `Dimension.name`. This will not be supported in the future, please report as an issue. 
  return next(i for i, d in enumerate(dimensions) if d == dim)
/home/docs/.local/share/hatch/env/virtual/hv-anndata/STk7F69l/docs/lib/python3.13/site-packages/holoviews/core/data/grid.py:326: FutureWarning: Probably comparing to a dimension created from `Dimension.name`. This will not be supported in the future, please report as an issue. 
  if d not in dataset.kdims+virtual_coords]
/home/docs/.local/share/hatch/env/virtual/hv-anndata/STk7F69l/docs/lib/python3.13/site-packages/holoviews/core/dimension.py:1073: FutureWarning: Probably comparing to a dimension created from `Dimension.name`. This will not be supported in the future, please report as an issue. 
  return next(i for i, d in enumerate(dimensions) if d == dim)
/home/docs/.local/share/hatch/env/virtual/hv-anndata/STk7F69l/docs/lib/python3.13/site-packages/holoviews/core/data/grid.py:326: FutureWarning: Probably comparing to a dimension created from `Dimension.name`. This will not be supported in the future, please report as an issue. 
  if d not in dataset.kdims+virtual_coords]
/home/docs/.local/share/hatch/env/virtual/hv-anndata/STk7F69l/docs/lib/python3.13/site-packages/holoviews/core/dimension.py:1073: FutureWarning: Probably comparing to a dimension created from `Dimension.name`. This will not be supported in the future, please report as an issue. 
  return next(i for i, d in enumerate(dimensions) if d == dim)
/home/docs/.local/share/hatch/env/virtual/hv-anndata/STk7F69l/docs/lib/python3.13/site-packages/holoviews/core/data/grid.py:326: FutureWarning: Probably comparing to a dimension created from `Dimension.name`. This will not be supported in the future, please report as an issue. 
  if d not in dataset.kdims+virtual_coords]
/home/docs/.local/share/hatch/env/virtual/hv-anndata/STk7F69l/docs/lib/python3.13/site-packages/holoviews/core/dimension.py:1073: FutureWarning: Probably comparing to a dimension created from `Dimension.name`. This will not be supported in the future, please report as an issue. 
  return next(i for i, d in enumerate(dimensions) if d == dim)
/home/docs/.local/share/hatch/env/virtual/hv-anndata/STk7F69l/docs/lib/python3.13/site-packages/holoviews/core/data/grid.py:326: FutureWarning: Probably comparing to a dimension created from `Dimension.name`. This will not be supported in the future, please report as an issue. 
  if d not in dataset.kdims+virtual_coords]
/home/docs/.local/share/hatch/env/virtual/hv-anndata/STk7F69l/docs/lib/python3.13/site-packages/holoviews/core/dimension.py:1073: FutureWarning: Probably comparing to a dimension created from `Dimension.name`. This will not be supported in the future, please report as an issue. 
  return next(i for i, d in enumerate(dimensions) if d == dim)
/home/docs/.local/share/hatch/env/virtual/hv-anndata/STk7F69l/docs/lib/python3.13/site-packages/holoviews/core/data/grid.py:326: FutureWarning: Probably comparing to a dimension created from `Dimension.name`. This will not be supported in the future, please report as an issue. 
  if d not in dataset.kdims+virtual_coords]
/home/docs/.local/share/hatch/env/virtual/hv-anndata/STk7F69l/docs/lib/python3.13/site-packages/holoviews/core/dimension.py:1073: FutureWarning: Probably comparing to a dimension created from `Dimension.name`. This will not be supported in the future, please report as an issue. 
  return next(i for i, d in enumerate(dimensions) if d == dim)
/home/docs/.local/share/hatch/env/virtual/hv-anndata/STk7F69l/docs/lib/python3.13/site-packages/holoviews/core/dimension.py:1073: FutureWarning: Probably comparing to a dimension created from `Dimension.name`. This will not be supported in the future, please report as an issue. 
  return next(i for i, d in enumerate(dimensions) if d == dim)
/home/docs/.local/share/hatch/env/virtual/hv-anndata/STk7F69l/docs/lib/python3.13/site-packages/holoviews/core/data/grid.py:326: FutureWarning: Probably comparing to a dimension created from `Dimension.name`. This will not be supported in the future, please report as an issue. 
  if d not in dataset.kdims+virtual_coords]
/home/docs/.local/share/hatch/env/virtual/hv-anndata/STk7F69l/docs/lib/python3.13/site-packages/holoviews/core/dimension.py:1073: FutureWarning: Probably comparing to a dimension created from `Dimension.name`. This will not be supported in the future, please report as an issue. 
  return next(i for i, d in enumerate(dimensions) if d == dim)
/home/docs/.local/share/hatch/env/virtual/hv-anndata/STk7F69l/docs/lib/python3.13/site-packages/holoviews/core/data/grid.py:326: FutureWarning: Probably comparing to a dimension created from `Dimension.name`. This will not be supported in the future, please report as an issue. 
  if d not in dataset.kdims+virtual_coords]