hv_anndata.plotting.scanpy.heatmap

hv_anndata.plotting.scanpy.heatmap(adata, base=A.X, /, vdims=(), *, transpose=False, add_dendrogram=False)

Shortcut for a heatmap.

Basically just

>>> hv.HeatMap(adata, [A.obs.index, A.var.index], [base[:, :], *vdims]).opts(...)

Set base to e.g. A or A.layers[key], and transpose=True to switch the order of the dims.

If add_dendrogram is True, the dendrogram is added. Call it directly to customize the dendrogram:

>>> hv.operation.dendrogram(heatmap, adjoint_dims=..., main_dim=base[:, :])
Parameters:
adata AnnData

The AnnData object.

base LayerAcc | GraphAcc, default: A.X

The base layer/graph of the heatmap.

vdims Collection[AdDim], default: ()

The value dimensions.

transpose bool, default: False

Whether to transpose the dims.

add_dendrogram bool | Literal['obs', 'var'], default: False

Where to add dendrograms to the heatmap: True for both, "obs"/"var" for one, and False for none.

Return type:

HeatMap

Returns:

A heatmap object

Examples

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

register()

adata = data.pbmc68k_processed()
markers = ["C1QA", "PSAP", "CD79A", "CD79B", "CST3", "LYZ"]
hv_sc.heatmap(
    adata[:, markers], A.X, [A.obs["n_counts"]], add_dendrogram="obs"
).opts(hv.opts.HeatMap(xticks=0, aspect=2))

/home/docs/.local/share/hatch/env/virtual/hv-anndata/STk7F69l/docs/lib/python3.13/site-packages/holoviews/operation/element.py:1365: 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 self.p.adjoint_dims:

/home/docs/.local/share/hatch/env/virtual/hv-anndata/STk7F69l/docs/lib/python3.13/site-packages/holoviews/core/dimension.py:1033: FutureWarning: Probably comparing to a dimension created from `Dimension.name`. This will not be supported in the future, please report as an issue. 
  dims = [d for d in all_dims if dimension == d]
/home/docs/.local/share/hatch/env/virtual/hv-anndata/STk7F69l/docs/lib/python3.13/site-packages/holoviews/operation/element.py:1406: FutureWarning: Probably comparing to a dimension created from `Dimension.name`. This will not be supported in the future, please report as an issue. 
  if dim not in self.p.adjoint_dims:

/home/docs/.local/share/hatch/env/virtual/hv-anndata/STk7F69l/docs/lib/python3.13/site-packages/holoviews/core/data/xarray.py:183: FutureWarning: Probably comparing to a dimension created from `Dimension.name`. This will not be supported in the future, please report as an issue. 
  data = {d: np.asarray(values) if d in kdims else values
/home/docs/.local/share/hatch/env/virtual/hv-anndata/STk7F69l/docs/lib/python3.13/site-packages/holoviews/core/data/xarray.py:230: FutureWarning: Probably comparing to a dimension created from `Dimension.name`. This will not be supported in the future, please report as an issue. 
  if c in kdims or len(da[c].shape) != 1 or da[c].shape[0] <= 1:
/home/docs/.local/share/hatch/env/virtual/hv-anndata/STk7F69l/docs/lib/python3.13/site-packages/holoviews/core/data/xarray.py:387: FutureWarning: Probably comparing to a dimension created from `Dimension.name`. This will not be supported in the future, please report as an issue. 
  if dim in dataset.kdims:
/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/xarray.py:387: FutureWarning: Probably comparing to a dimension created from `Dimension.name`. This will not be supported in the future, please report as an issue. 
  if dim in dataset.kdims:
/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/xarray.py:387: FutureWarning: Probably comparing to a dimension created from `Dimension.name`. This will not be supported in the future, please report as an issue. 
  if dim in dataset.kdims:
/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/xarray.py:387: FutureWarning: Probably comparing to a dimension created from `Dimension.name`. This will not be supported in the future, please report as an issue. 
  if dim in dataset.kdims:
/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]

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

register()

adata = data.pbmc68k_processed()
markers = ["C1QA", "PSAP", "CD79A", "CD79B", "CST3", "LYZ"]
hv_sc.heatmap(
    adata[:, markers], A.X, [A.obs["n_counts"]], add_dendrogram="obs"
).opts(hv.opts.HeatMap(xticks=0, aspect=2))

/home/docs/.local/share/hatch/env/virtual/hv-anndata/STk7F69l/docs/lib/python3.13/site-packages/holoviews/operation/element.py:1365: 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 self.p.adjoint_dims:

/home/docs/.local/share/hatch/env/virtual/hv-anndata/STk7F69l/docs/lib/python3.13/site-packages/holoviews/core/dimension.py:1033: FutureWarning: Probably comparing to a dimension created from `Dimension.name`. This will not be supported in the future, please report as an issue. 
  dims = [d for d in all_dims if dimension == d]
/home/docs/.local/share/hatch/env/virtual/hv-anndata/STk7F69l/docs/lib/python3.13/site-packages/holoviews/operation/element.py:1406: FutureWarning: Probably comparing to a dimension created from `Dimension.name`. This will not be supported in the future, please report as an issue. 
  if dim not in self.p.adjoint_dims:

/home/docs/.local/share/hatch/env/virtual/hv-anndata/STk7F69l/docs/lib/python3.13/site-packages/holoviews/core/data/xarray.py:183: FutureWarning: Probably comparing to a dimension created from `Dimension.name`. This will not be supported in the future, please report as an issue. 
  data = {d: np.asarray(values) if d in kdims else values
/home/docs/.local/share/hatch/env/virtual/hv-anndata/STk7F69l/docs/lib/python3.13/site-packages/holoviews/core/data/xarray.py:230: FutureWarning: Probably comparing to a dimension created from `Dimension.name`. This will not be supported in the future, please report as an issue. 
  if c in kdims or len(da[c].shape) != 1 or da[c].shape[0] <= 1:
/home/docs/.local/share/hatch/env/virtual/hv-anndata/STk7F69l/docs/lib/python3.13/site-packages/holoviews/core/data/xarray.py:387: FutureWarning: Probably comparing to a dimension created from `Dimension.name`. This will not be supported in the future, please report as an issue. 
  if dim in dataset.kdims:
/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/xarray.py:387: FutureWarning: Probably comparing to a dimension created from `Dimension.name`. This will not be supported in the future, please report as an issue. 
  if dim in dataset.kdims:
/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/xarray.py:387: FutureWarning: Probably comparing to a dimension created from `Dimension.name`. This will not be supported in the future, please report as an issue. 
  if dim in dataset.kdims:
/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/xarray.py:387: FutureWarning: Probably comparing to a dimension created from `Dimension.name`. This will not be supported in the future, please report as an issue. 
  if dim in dataset.kdims:
/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]

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

register()

adata = data.pbmc68k_processed()
markers = ["C1QA", "PSAP", "CD79A", "CD79B", "CST3", "LYZ"]
hv_sc.heatmap(
    adata[:, markers], A.X, [A.obs["n_counts"]], add_dendrogram="obs"
).opts(hv.opts.HeatMap(xticks=0, aspect=2))

/home/docs/.local/share/hatch/env/virtual/hv-anndata/STk7F69l/docs/lib/python3.13/site-packages/holoviews/operation/element.py:1365: 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 self.p.adjoint_dims:

/home/docs/.local/share/hatch/env/virtual/hv-anndata/STk7F69l/docs/lib/python3.13/site-packages/holoviews/core/dimension.py:1033: FutureWarning: Probably comparing to a dimension created from `Dimension.name`. This will not be supported in the future, please report as an issue. 
  dims = [d for d in all_dims if dimension == d]
/home/docs/.local/share/hatch/env/virtual/hv-anndata/STk7F69l/docs/lib/python3.13/site-packages/holoviews/operation/element.py:1406: FutureWarning: Probably comparing to a dimension created from `Dimension.name`. This will not be supported in the future, please report as an issue. 
  if dim not in self.p.adjoint_dims:

/home/docs/.local/share/hatch/env/virtual/hv-anndata/STk7F69l/docs/lib/python3.13/site-packages/holoviews/core/data/xarray.py:183: FutureWarning: Probably comparing to a dimension created from `Dimension.name`. This will not be supported in the future, please report as an issue. 
  data = {d: np.asarray(values) if d in kdims else values
/home/docs/.local/share/hatch/env/virtual/hv-anndata/STk7F69l/docs/lib/python3.13/site-packages/holoviews/core/data/xarray.py:230: FutureWarning: Probably comparing to a dimension created from `Dimension.name`. This will not be supported in the future, please report as an issue. 
  if c in kdims or len(da[c].shape) != 1 or da[c].shape[0] <= 1:
/home/docs/.local/share/hatch/env/virtual/hv-anndata/STk7F69l/docs/lib/python3.13/site-packages/holoviews/core/data/xarray.py:387: FutureWarning: Probably comparing to a dimension created from `Dimension.name`. This will not be supported in the future, please report as an issue. 
  if dim in dataset.kdims:
/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/xarray.py:387: FutureWarning: Probably comparing to a dimension created from `Dimension.name`. This will not be supported in the future, please report as an issue. 
  if dim in dataset.kdims:
/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)
WARNING:param.LayoutPlot56113: Plotly plotting class for Empty type not found, object will not be rendered.

WARNING:param.LayoutPlot56113: Plotly plotting class for Dendrogram type not found, object will not be rendered.

/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]