hv_anndata.plotting.scanpy.highly_variable_genes

hv_anndata.plotting.scanpy.highly_variable_genes(adata)

Plot dispersions used to identify highly variable genes.

Parameters:
adata AnnData

The AnnData object.

Return type:

Layout

Returns:

A layout containing two Scatter plots, one normalized and one not.

Examples

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

register()

adata = data.pbmc68k_processed()
sc.pp.highly_variable_genes(adata)

hv_sc.highly_variable_genes(adata)

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

register()

adata = data.pbmc68k_processed()
sc.pp.highly_variable_genes(adata)

hv_sc.highly_variable_genes(adata)
ValueError: 'color' kwarg must be a color or sequence of color specs. For a sequence of val ...
Traceback (most recent call last): File "/home/docs/.local/share/hatch/env/virtual/hv-anndata/STk7F69l/docs/lib/python3.13/site-packages/matplotlib/axes/_axes.py", line 4692, in _parse_scatter_color_args mcolors.to_rgba_array(kwcolor) ~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^ File "/home/docs/.local/share/hatch/env/virtual/hv-anndata/STk7F69l/docs/lib/python3.13/site-packages/matplotlib/colors.py", line 515, in to_rgba_array rgba = np.array([to_rgba(cc) for cc in c]) ~~~~~~~^^^^ File "/home/docs/.local/share/hatch/env/virtual/hv-anndata/STk7F69l/docs/lib/python3.13/site-packages/matplotlib/colors.py", line 317, in to_rgba rgba = _to_rgba_no_colorcycle(c, alpha) File "/home/docs/.local/share/hatch/env/virtual/hv-anndata/STk7F69l/docs/lib/python3.13/site-packages/matplotlib/colors.py", line 401, in _to_rgba_no_colorcycle raise ValueError(f"Invalid RGBA argument: {orig_c!r}") ValueError: Invalid RGBA argument: np.True_ The above exception was the direct cause of the following exception: Traceback (most recent call last): File "/home/docs/.local/share/hatch/env/virtual/hv-anndata/STk7F69l/docs/lib/python3.13/site-packages/holoviews/plotting/mpl/element.py", line 617, in render_artists handles = self.init_artists(ax, plot_data, plot_kwargs) File "/home/docs/.local/share/hatch/env/virtual/hv-anndata/STk7F69l/docs/lib/python3.13/site-packages/holoviews/plotting/mpl/element.py", line 666, in init_artists artist = plot_fn(*plot_args, **plot_kwargs) File "/home/docs/.local/share/hatch/env/virtual/hv-anndata/STk7F69l/docs/lib/python3.13/site-packages/matplotlib/_api/deprecation.py", line 453, in wrapper return func(*args, **kwargs) File "/home/docs/.local/share/hatch/env/virtual/hv-anndata/STk7F69l/docs/lib/python3.13/site-packages/matplotlib/__init__.py", line 1524, in inner return func( ax, *map(cbook.sanitize_sequence, args), **{k: cbook.sanitize_sequence(v) for k, v in kwargs.items()}) File "/home/docs/.local/share/hatch/env/virtual/hv-anndata/STk7F69l/docs/lib/python3.13/site-packages/matplotlib/axes/_axes.py", line 4954, in scatter self._parse_scatter_color_args( ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ c, edgecolors, kwargs, x.size, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ get_next_color_func=self._get_patches_for_fill.get_next_color) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/docs/.local/share/hatch/env/virtual/hv-anndata/STk7F69l/docs/lib/python3.13/site-packages/matplotlib/axes/_axes.py", line 4694, in _parse_scatter_color_args raise ValueError( ...<2 lines>... "the 'c' argument instead.") from err ValueError: 'color' kwarg must be a color or sequence of color specs. For a sequence of values to be color-mapped, use the 'c' argument instead. 
import scanpy as sc
import hv_anndata.plotting.scanpy as hv_sc
from hv_anndata import data, register, A

register()

adata = data.pbmc68k_processed()
sc.pp.highly_variable_genes(adata)

hv_sc.highly_variable_genes(adata)

WARNING:param.main: Option 'legend_labels' for Scatter type not valid for selected backend ('plotly'). Option only applies to following backends: ['bokeh', 'matplotlib']

WARNING:param.main: Option 'legend_position' for Scatter type not valid for selected backend ('plotly'). Option only applies to following backends: ['bokeh', 'matplotlib']

WARNING:param.main: Option 'legend_labels' for Scatter type not valid for selected backend ('plotly'). Option only applies to following backends: ['bokeh', 'matplotlib']

WARNING:param.main: Option 'legend_position' for Scatter type not valid for selected backend ('plotly'). Option only applies to following backends: ['bokeh', 'matplotlib']