scanpy.pl.paga_compare

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scanpy.pl.paga_compare#

scanpy.pl.paga_compare(adata, basis=None, *, edges=False, color=None, alpha=None, groups=None, components=None, projection='2d', legend_loc='on data', legend_fontsize=None, legend_fontweight='bold', legend_fontoutline=None, color_map=None, palette=None, frameon=False, size=None, title=None, right_margin=None, left_margin=0.05, show=None, save=None, title_graph=None, groups_graph=None, pos=None, **paga_graph_params)[source]#

Scatter and PAGA graph side-by-side.

Consists in a scatter plot and the abstracted graph. See paga() for all related parameters.

See paga_path() for visualizing gene changes along paths through the abstracted graph.

Additional parameters are as follows.

Parameters:
adata AnnData

Annotated data matrix.

kwds_scatter

Keywords for scatter().

kwds_paga

Keywords for paga().

Returns:

A list of Axes if show is False.

Examples

Compute a PAGA graph on the bundled PBMC dataset and show it next to the UMAP embedding.

import scanpy as sc
adata = sc.datasets.pbmc68k_reduced()
sc.tl.paga(adata, groups="bulk_labels")
sc.pl.paga_compare(adata, basis="umap")
../../_images/scanpy-pl-paga_compare-1.png
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