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Add example PCA plots #1813

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merged 5 commits into from
May 3, 2021
Merged

Add example PCA plots #1813

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5b02ba2
Add example PCA plots
lazappi Apr 27, 2021
dbd10e8
fix docs
giovp May 3, 2021
f033ee4
add see also
giovp May 3, 2021
dd61342
fix see also
giovp May 3, 2021
078ce3e
revert see also
giovp May 3, 2021
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31 changes: 31 additions & 0 deletions scanpy/plotting/_tools/scatterplots.py
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Expand Up @@ -740,6 +740,37 @@ def pca(
Returns
-------
If `show==False` a :class:`~matplotlib.axes.Axes` or a list of it.

Examples
--------

.. plot::
:context: close-figs

import scanpy as sc
adata = sc.datasets.pbmc3k_processed()
sc.pl.pca(adata)

Colour points by discrete variable (Louvain clusters).

.. plot::
:context: close-figs

sc.pl.pca(adata, color="louvain")

Colour points by gene expression.

.. plot::
:context: close-figs

sc.pl.pca(adata, color="CST3")

.. currentmodule:: scanpy

See also
--------
tl.pca
pp.pca
"""
if not annotate_var_explained:
return embedding(
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