.. module:: scanpy
.. automodule:: scanpy :noindex:
Import Scanpy as:
import scanpy as sc
Note
Additional functionality is available in the broader :doc:`ecosystem <../ecosystem>`, with some tools being wrapped in the :mod:`scanpy.external` module.
.. module:: scanpy.pp
.. currentmodule:: scanpy
Filtering of highly-variable genes, batch-effect correction, per-cell normalization, preprocessing recipes.
Any transformation of the data matrix that is not a tool. Other than tools, preprocessing steps usually don't return an easily interpretable annotation, but perform a basic transformation on the data matrix.
For visual quality control, see :func:`~scanpy.pl.highest_expr_genes` and :func:`~scanpy.pl.filter_genes_dispersion` in :mod:`scanpy.pl`.
.. autosummary:: :toctree: generated/ pp.calculate_qc_metrics pp.filter_cells pp.filter_genes pp.highly_variable_genes pp.log1p pp.pca pp.normalize_total pp.regress_out pp.scale pp.subsample pp.downsample_counts
.. autosummary:: :toctree: generated/ pp.recipe_zheng17 pp.recipe_weinreb17 pp.recipe_seurat
Also see Data integration. Note that a simple batch correction method is available via :func:`pp.regress_out`. Checkout :mod:`scanpy.external` for more.
.. autosummary:: :toctree: generated/ pp.combat
.. autosummary:: :toctree: generated/ pp.neighbors
.. module:: scanpy.tl
.. currentmodule:: scanpy
Any transformation of the data matrix that is not preprocessing. In contrast to a preprocessing function, a tool usually adds an easily interpretable annotation to the data matrix, which can then be visualized with a corresponding plotting function.
.. autosummary:: :toctree: generated/ tl.pca tl.tsne tl.umap tl.draw_graph tl.diffmap
Compute densities on embeddings.
.. autosummary:: :toctree: generated/ tl.embedding_density
.. autosummary:: :toctree: generated/ tl.leiden tl.louvain tl.dendrogram tl.dpt tl.paga
.. autosummary:: :toctree: generated/ tl.ingest
.. autosummary:: :toctree: generated/ tl.rank_genes_groups tl.filter_rank_genes_groups tl.marker_gene_overlap
.. autosummary:: :toctree: generated/ tl.score_genes tl.score_genes_cell_cycle
.. autosummary:: :toctree: generated/ tl.sim
.. module:: scanpy.pl
.. currentmodule:: scanpy
The plotting module :mod:`scanpy.pl` largely parallels the tl.* and a few of the pp.* functions.
For most tools and for some preprocessing functions, you'll find a plotting function with the same name.
See :tutorial:`plotting/core` for an overview of how to use these functions.
Note
See the :ref:`settings` section for all important plotting configurations.
.. autosummary:: :toctree: generated/ pl.scatter pl.heatmap pl.dotplot pl.tracksplot pl.violin pl.stacked_violin pl.matrixplot pl.clustermap pl.ranking pl.dendrogram
These classes allow fine tuning of visual parameters.
.. autosummary::
:toctree: generated/classes
pl.DotPlot
pl.MatrixPlot
pl.StackedViolin
Methods for visualizing quality control and results of preprocessing functions.
.. autosummary:: :toctree: generated/ pl.highest_expr_genes pl.filter_genes_dispersion pl.highly_variable_genes
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.
.. autosummary:: :toctree: generated/ pl.pca pl.pca_loadings pl.pca_variance_ratio pl.pca_overview
.. autosummary:: :toctree: generated/ pl.tsne pl.umap pl.diffmap pl.draw_graph pl.spatial pl.embedding
Compute densities on embeddings.
.. autosummary:: :toctree: generated/ pl.embedding_density
Visualize clusters using one of the embedding methods passing color='louvain'.
.. autosummary:: :toctree: generated/ pl.dpt_groups_pseudotime pl.dpt_timeseries pl.paga pl.paga_path pl.paga_compare
.. autosummary:: :toctree: generated/ 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
.. autosummary:: :toctree: generated/ pl.sim
Note
For reading annotation use :ref:`pandas.read_… <pandas:io>` and add it to your :class:`anndata.AnnData` object. The following read functions are intended for the numeric data in the data matrix X.
Read common file formats using
.. autosummary:: :toctree: generated/ read
Read 10x formatted hdf5 files and directories containing .mtx files using
.. autosummary:: :toctree: generated/ read_10x_h5 read_10x_mtx read_visium
Read other formats using functions borrowed from :mod:`anndata`
.. autosummary:: :toctree: generated/ read_h5ad read_csv read_excel read_hdf read_loom read_mtx read_text read_umi_tools
.. module:: scanpy.get
.. currentmodule:: scanpy
The module sc.get provides convenience functions for getting values back in useful formats.
.. autosummary:: :toctree: generated/ get.obs_df get.var_df get.rank_genes_groups_df
.. module:: scanpy.queries
.. currentmodule:: scanpy
This module provides useful queries for annotation and enrichment.
.. autosummary:: :toctree: generated/ queries.biomart_annotations queries.gene_coordinates queries.mitochondrial_genes queries.enrich
.. module:: scanpy.metrics
.. currentmodule:: scanpy
Collections of useful measurements for evaluating results.
.. autosummary:: :toctree: generated/ metrics.confusion_matrix metrics.gearys_c metrics.morans_i
:class:`~anndata.AnnData` is reexported from :mod:`anndata`.
Represent data as a neighborhood structure, usually a knn graph.
.. autosummary:: :toctree: generated/ Neighbors
A convenience function for setting some default :obj:`matplotlib.rcParams` and a high-resolution jupyter display backend useful for use in notebooks.
.. autosummary:: :toctree: generated/ set_figure_params
An instance of the :class:`~scanpy._settings.ScanpyConfig` is available as scanpy.settings and allows configuring Scanpy.
.. autosummary:: :toctree: generated/ _settings.ScanpyConfig
Some selected settings are discussed in the following.
Influence the global behavior of plotting functions. In non-interactive scripts,
you'd usually want to set settings.autoshow to False.
.. autosummary:: ~_settings.ScanpyConfig.autoshow ~_settings.ScanpyConfig.autosave
The default directories for saving figures, caching files and storing datasets.
.. autosummary:: ~_settings.ScanpyConfig.figdir ~_settings.ScanpyConfig.cachedir ~_settings.ScanpyConfig.datasetdir
The verbosity of logging output, where verbosity levels have the following meaning: 0='error', 1='warning', 2='info', 3='hint', 4=more details, 5=even more details, etc.
.. autosummary:: ~_settings.ScanpyConfig.verbosity
Print versions of packages that might influence numerical results.
.. autosummary:: :toctree: generated/ logging.print_header logging.print_versions
.. module:: scanpy.datasets
.. currentmodule:: scanpy
.. autosummary:: :toctree: generated/ datasets.blobs datasets.ebi_expression_atlas datasets.krumsiek11 datasets.moignard15 datasets.pbmc3k datasets.pbmc3k_processed datasets.pbmc68k_reduced datasets.paul15 datasets.toggleswitch datasets.visium_sge
.. autosummary:: :toctree: generated/ pp.filter_genes_dispersion pp.normalize_per_cell