Repository: scverse/scanpy

Issue:
Plotting functions should show up in table of contents
It would be useful for plotting functions to show up in the table of contents for the API section of the docs, like they do for all other functions

<img width="303" alt="image" src="https://user-images.githubusercontent.com/8238804/108953042-a213c300-76be-11eb-94c6-51d7829fb6ec.png">


<img width="303" alt="image" src="https://user-images.githubusercontent.com/8238804/108953055-a93ad100-76be-11eb-8702-94879bbb53dd.png">



Discussion:

Resolving patch:
diff --git a/scanpy/external/__init__.py b/scanpy/external/__init__.py
--- a/scanpy/external/__init__.py
+++ b/scanpy/external/__init__.py
@@ -8,114 +8,3 @@
 
 _utils.annotate_doc_types(sys.modules[__name__], 'scanpy')
 del sys, _utils
-
-
-__doc__ = """\
-External API
-============
-
-.. note::
-   More tools that integrate well with scanpy and anndata can be found on the :doc:`ecosystem page <../ecosystem>`.
-
-Import Scanpy's wrappers to external tools as::
-
-   import scanpy.external as sce
-
-If you'd like to include a tool here, consider making a pull request (:doc:`instructions <../dev/external-tools>`).
-If the tool already uses `scanpy` or `anndata`, it may fit better in the :doc:`ecosystem page <../ecosystem>`.
-
-Preprocessing: PP
-------------------
-
-Data integration
-~~~~~~~~~~~~~~~~
-
-.. autosummary::
-   :toctree: .
-
-   pp.bbknn
-   pp.harmony_integrate
-   pp.mnn_correct
-   pp.scanorama_integrate
-
-
-Sample demultiplexing, Doublet detection
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-.. autosummary::
-   :toctree: .
-
-   pp.scrublet
-   pp.scrublet_simulate_doublets
-   pl.scrublet_score_distribution
-   pp.hashsolo
-
-Imputation
-~~~~~~~~~~
-
-Note that the fundamental limitations of imputation are still under `debate
-<https://github.com/theislab/scanpy/issues/189>`__.
-
-.. autosummary::
-   :toctree: .
-
-   pp.dca
-   pp.magic
-
-
-Tools: TL
-----------
-
-Embeddings
-~~~~~~~~~~
-
-.. autosummary::
-   :toctree: .
-
-   tl.phate
-   tl.palantir
-   tl.trimap
-   tl.sam
-
-Clustering and trajectory inference
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-.. autosummary::
-   :toctree: .
-
-   tl.phenograph
-   tl.harmony_timeseries
-   tl.wishbone
-   tl.palantir
-   tl.palantir_results
-
-Gene scores, Cell cycle
-~~~~~~~~~~~~~~~~~~~~~~~
-
-.. autosummary::
-   :toctree: .
-
-   tl.sandbag
-   tl.cyclone
-
-
-Plotting: PL
-------------
-
-.. autosummary::
-   :toctree: .
-
-   pl.phate
-   pl.trimap
-   pl.sam
-   pl.wishbone_marker_trajectory
-
-Exporting
----------
-
-.. autosummary::
-   :toctree: .
-
-   exporting.spring_project
-   exporting.cellbrowser
-"""
diff --git a/scanpy/plotting/__init__.py b/scanpy/plotting/__init__.py
--- a/scanpy/plotting/__init__.py
+++ b/scanpy/plotting/__init__.py
@@ -43,129 +43,3 @@
 from ._utils import timeseries, timeseries_subplot, timeseries_as_heatmap
 
 from ._qc import highest_expr_genes
-
-
-__doc__ = """\
-Plotting API
-============
-
-.. currentmodule:: scanpy
-
-.. note::
-   See the :ref:`settings` section for all important plotting configurations.
-
-.. _pl-generic:
-
-Generic
--------
-
-.. autosummary::
-   :toctree: .
-
-   pl.scatter
-   pl.heatmap
-   pl.dotplot
-   pl.tracksplot
-   pl.violin
-   pl.stacked_violin
-   pl.matrixplot
-   pl.clustermap
-   pl.ranking
-   pl.dendrogram
-
-
-Classes
--------
-
-These classes allow fine tuning of visual parameters.
-
-.. autosummary::
-   :toctree: .
-
-    pl.DotPlot
-    pl.MatrixPlot
-    pl.StackedViolin
-
-
-Preprocessing
--------------
-
-Methods for visualizing quality control and results of preprocessing functions.
-
-.. autosummary::
-   :toctree: .
-
-   pl.highest_expr_genes
-   pl.filter_genes_dispersion
-   pl.highly_variable_genes
-
-
-Tools
------
-
-Methods that extract and visualize tool-specific annotation in an
-:class:`~anndata.AnnData` object.  For any method in module ``tl``, there is
-a method with the same name in ``pl``.
-
-PCA
-~~~
-.. autosummary::
-   :toctree: .
-
-   pl.pca
-   pl.pca_loadings
-   pl.pca_variance_ratio
-   pl.pca_overview
-
-Embeddings
-~~~~~~~~~~
-.. autosummary::
-   :toctree: .
-
-   pl.tsne
-   pl.umap
-   pl.diffmap
-   pl.draw_graph
-   pl.spatial
-   pl.embedding
-
-Compute densities on embeddings.
-
-.. autosummary::
-   :toctree: .
-
-   pl.embedding_density
-
-Branching trajectories and pseudotime, clustering
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-Visualize clusters using one of the embedding methods passing ``color='louvain'``.
-
-.. autosummary::
-   :toctree: .
-
-   pl.dpt_groups_pseudotime
-   pl.dpt_timeseries
-   pl.paga
-   pl.paga_path
-   pl.paga_compare
-
-Marker genes
-~~~~~~~~~~~~
-.. autosummary::
-   :toctree: .
-
-   pl.rank_genes_groups
-   pl.rank_genes_groups_violin
-   pl.rank_genes_groups_stacked_violin
-   pl.rank_genes_groups_heatmap
-   pl.rank_genes_groups_dotplot
-   pl.rank_genes_groups_matrixplot
-   pl.rank_genes_groups_tracksplot
-
-Simulations
-~~~~~~~~~~~
-.. autosummary::
-   :toctree: .
-
-   pl.sim
-"""


Test patch: