text: """\
  API
  ===
  
  Import Scanpy's high-level API as::
  
     import scanpy.api as sc
  
  Preprocessing: PP
  ------------------
  
  Filtering of highly-variable genes, batch-effect correction, per-cell (UMI) normalization, preprocessing recipes.
  
  **Basic Preprocessing**
  
  .. autosummary::
     :toctree: .
  
     pp.filter_cells
     pp.filter_genes
     pp.filter_genes_dispersion
     pp.log1p
     pp.pca
     pp.normalize_per_cell
     pp.regress_out
     pp.scale
     pp.subsample
     pp.downsample_counts
  
  **Recipes**
  
  .. autosummary::
     :toctree: .
  
     pp.recipe_zheng17
     pp.recipe_weinreb16
  
  
  Tools: TL
  ----------
  
  **Embeddings**
  
  .. autosummary::
     :toctree: .
  
     tl.pca
     tl.tsne
     tl.umap
     tl.diffmap
     tl.draw_graph
  
  **Branching trajectories and pseudotime, clustering, differential expression**
  
  .. autosummary::
     :toctree: .
  
     tl.aga
     tl.louvain
     tl.dpt
     tl.rank_genes_groups
  
  **Gene scores, gene correlation**
  
  .. autosummary::
     :toctree: .
  
     tl.score_genes
     tl.score_genes_cell_cycle
  
  **Simulations**
  
  .. autosummary::
     :toctree: .
  
     tl.sim
  
  
  Reading and Writing
  -------------------
  
  *Note:* For reading annotation use
  `pandas.read_… <http://pandas.pydata.org/pandas-docs/stable/io.html>`_ and add
  it to your `AnnData` object. The following read functions are intended for
  the numeric data in the data matrix `X`.
  
  Read common file formats using
  
  .. autosummary::
     :toctree: .
  
     read
  
  Read 10x formatted hdf5 files using
  
  .. autosummary::
     :toctree: .
  
     read_10x_h5
  
  Read other formats using functions borrowed from `anndata
  <http://anndata.readthedocs.io>`_
  
  .. autosummary::
     :toctree: .
  
     read_h5ad
     read_csv
     read_excel
     read_hdf
     read_loom
     read_mtx
     read_text
     read_umi_tools
  
  For writing, use `AnnData.write_… <http://anndata.readthedocs.io/en/latest/api.html>`_.
  
  
  Exporting
  ---------
  
  .. autosummary::
     :toctree: .
  
     export_to.spring_project
  
  
  Datasets
  --------
  
  .. autosummary::
     :toctree: .
  
     datasets.blobs
     datasets.krumsiek11
     datasets.moignard15
     datasets.paul15
     datasets.paul15_raw
     datasets.toggleswitch
  
  
  Plotting: PL
  -------------
  
  .. autosummary::
     :toctree: .
  
     pl.set_rcParams_Scanpy
     pl.set_rcParams_Defaults
  
  .. raw:: html
  
  **Generic plotting with AnnData**
  
  .. autosummary::
     :toctree: .
  
     pl.scatter
     pl.ranking
  
  Thin wrappers for Seaborn functions.
  
  .. autosummary::
     :toctree: .
  
     pl.violin
     pl.clustermap
  
  **Plotting tool results**
  
  Methods that extract and visualize tool-specific annotation in an AnnData object.
  For any method in module `tl`, there is a method with the same name in `pl`.
  
  *Embeddings*
  
  .. autosummary::
     :toctree: .
  
     pl.pca
     pl.pca_loadings
     pl.pca_scatter
     pl.pca_variance_ratio
     pl.tsne
     pl.umap
     pl.diffmap
     pl.draw_graph
  
  *Branching trajectories and pseudotime, clustering, differential expression*
  
  .. autosummary::
     :toctree: .
  
     pl.aga
     pl.aga_graph
     pl.aga_path
     pl.louvain
     pl.dpt
     pl.dpt_scatter
     pl.dpt_groups_pseudotime
     pl.dpt_timeseries
     pl.rank_genes_groups
     pl.rank_genes_groups_violin
  
  *Simulations*
  
  .. autosummary::
     :toctree: .
  
     pl.sim
  
  
  Settings
  --------
  
  Global settings.
  
  ==============================================  ===================================
  `settings.verbosity`                            Verbosity level (default: 1).
  `settings.file_format_figs`                     Format for saving figures (default: 'png').
  `settings.figdir`                               Default directory for saving figures (default: './figures').
  `settings.autoshow`                             Automatically show figures (default: `True`).
  `settings.autoshow`                             Automatically show figures (default: `True`).
  ==============================================  ===================================
  
  The verbosity levels have the following meaning:
  
  ===  ======================================
   0   Only show 'error' messages.
   1   Also show 'warning' messages.
   2   Also show 'info' messages.
   3   Also show 'hint' messages.
   4   Show very detailed progress.
  ...  Show even more detailed progress.
  ===  ======================================
  
  
  Logging
  -------
  
  ================================================  ===================================
  `logging.print_version_and_date()`                Print the version and the date.
  `logging.print_versions_dependencies_numerics()`  Print the versions of dependencies.
  ================================================  ===================================
  
  AnnData
  -------
  
  This only temporarily replicates the docs of `anndata
  <http://anndata.readthedocs.io>`_. Occurances of :class:`~scanpy.api.AnnData`
  will directly link to `anndata
  <http://anndata.readthedocs.io>`_ in the future.
  
  .. autosummary::
     :toctree: .
  
     AnnData
  """
  
  from anndata import AnnData
  from anndata import read as read_h5ad
  from anndata import read_csv, read_excel, read_hdf, read_loom, read_mtx, read_text, read_umi_tools
  
  from .. import __version__
  
  from .. import settings
  from .. import logging
  from . import tl
  tools = tl
  from . import pl
  plotting = pl
  from . import pp
  preprocessing = pp
  from ..readwrite import read, read_10x_h5, write, read_params, write_params
  from . import datasets
  from ..data_structs import DataGraph
  from .. import utils
  from . import export_to
  