Single-Cell Analysis in Python.

API

Import Scanpy as:

import scanpy as sc

Note

Additional functionality is available in the broader ecosystem, with some tools being wrapped in the scanpy.external module.

Preprocessing: pp

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.

Basic Preprocessing

For visual quality control, see highest_expr_genes() and filter_genes_dispersion() in scanpy.pl.

pp.calculate_qc_metrics(adata, *[, …])	Calculate quality control metrics.
pp.filter_cells(data[, min_counts, …])	Filter cell outliers based on counts and numbers of genes expressed.
pp.filter_genes(data[, min_counts, …])	Filter genes based on number of cells or counts.
pp.highly_variable_genes(adata[, layer, …])	Annotate highly variable genes [Satija15] [Zheng17] [Stuart19].
pp.log1p()	Logarithmize the data matrix.
pp.pca(data[, n_comps, zero_center, …])	Principal component analysis [Pedregosa11].
pp.normalize_total(adata[, target_sum, …])	Normalize counts per cell.
pp.regress_out(adata, keys[, n_jobs, copy])	Regress out (mostly) unwanted sources of variation.
pp.scale()	Scale data to unit variance and zero mean.
pp.subsample(data[, fraction, n_obs, …])	Subsample to a fraction of the number of observations.
pp.downsample_counts(adata[, …])	Downsample counts from count matrix.

Recipes

pp.recipe_zheng17(adata[, n_top_genes, log, …])	Normalization and filtering as of [Zheng17].
pp.recipe_weinreb17(adata[, log, …])	Normalization and filtering as of [Weinreb17].
pp.recipe_seurat(adata[, log, plot, copy])	Normalization and filtering as of Seurat [Satija15].

Batch effect correction

Also see Data integration. Note that a simple batch correction method is available via pp.regress_out(). Checkout scanpy.external for more.

pp.combat(adata[, key, covariates, inplace])

ComBat function for batch effect correction [Johnson07] [Leek12] [Pedersen12].

Neighbors

pp.neighbors(adata[, n_neighbors, n_pcs, …])

Compute a neighborhood graph of observations [McInnes18].

Tools: tl

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.

Embeddings

tl.pca(data[, n_comps, zero_center, …])	Principal component analysis [Pedregosa11].
tl.tsne(adata[, n_pcs, use_rep, perplexity, …])	t-SNE [Maaten08] [Amir13] [Pedregosa11].
tl.umap(adata[, min_dist, spread, …])	Embed the neighborhood graph using UMAP [McInnes18].
tl.draw_graph(adata[, layout, init_pos, …])	Force-directed graph drawing [Islam11] [Jacomy14] [Chippada18].
tl.diffmap(adata[, n_comps, neighbors_key, …])	Diffusion Maps [Coifman05] [Haghverdi15] [Wolf18].

Compute densities on embeddings.

tl.embedding_density(adata[, basis, …])

Calculate the density of cells in an embedding (per condition).

Clustering and trajectory inference

tl.leiden(adata[, resolution, restrict_to, …])	Cluster cells into subgroups [Traag18].
tl.louvain(adata[, resolution, …])	Cluster cells into subgroups [Blondel08] [Levine15] [Traag17].
tl.dendrogram(adata, groupby[, n_pcs, …])	Computes a hierarchical clustering for the given groupby categories.
tl.dpt(adata[, n_dcs, n_branchings, …])	Infer progression of cells through geodesic distance along the graph [Haghverdi16] [Wolf19].
tl.paga(adata[, groups, use_rna_velocity, …])	Mapping out the coarse-grained connectivity structures of complex manifolds [Wolf19].

Data integration

tl.ingest(adata, adata_ref[, obs, …])

Map labels and embeddings from reference data to new data.

Marker genes

tl.rank_genes_groups(adata, groupby[, …])	Rank genes for characterizing groups.
tl.filter_rank_genes_groups(adata[, key, …])	Filters out genes based on fold change and fraction of genes expressing the gene within and outside the groupby categories.
tl.marker_gene_overlap(adata, …[, key, …])	Calculate an overlap score between data-deriven marker genes and provided markers

Gene scores, Cell cycle

tl.score_genes(adata, gene_list[, …])	Score a set of genes [Satija15].
tl.score_genes_cell_cycle(adata, s_genes, …)	Score cell cycle genes [Satija15].

Simulations

tl.sim(model[, params_file, tmax, …])

Simulate dynamic gene expression data [Wittmann09] [Wolf18].

Plotting: pl

The plotting module 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 Settings section for all important plotting configurations.

Generic

pl.scatter(adata[, x, y, color, use_raw, …])	Scatter plot along observations or variables axes.
pl.heatmap(adata, var_names, groupby[, …])	Heatmap of the expression values of genes.
pl.dotplot(adata, var_names, groupby[, …])	Makes a dot plot of the expression values of var_names.
pl.tracksplot(adata, var_names, groupby[, …])	In this type of plot each var_name is plotted as a filled line plot where the y values correspond to the var_name values and x is each of the cells.
pl.violin(adata, keys[, groupby, log, …])	Violin plot.
pl.stacked_violin(adata, var_names, groupby)	Stacked violin plots.
pl.matrixplot(adata, var_names, groupby[, …])	Creates a heatmap of the mean expression values per group of each var_names.
pl.clustermap(adata[, obs_keys, use_raw, …])	Hierarchically-clustered heatmap.
pl.ranking(adata, attr, keys[, dictionary, …])	Plot rankings.
pl.dendrogram(adata, groupby, *[, …])	Plots a dendrogram of the categories defined in groupby.

Classes

These classes allow fine tuning of visual parameters.

pl.DotPlot(adata, var_names, groupby[, …])	Allows the visualization of two values that are encoded as dot size and color.
pl.MatrixPlot(adata, var_names, groupby[, …])	Allows the visualization of values using a color map.
pl.StackedViolin(adata, var_names, groupby)	Stacked violin plots.

Preprocessing

Methods for visualizing quality control and results of preprocessing functions.

pl.highest_expr_genes(adata[, n_top, show, …])	Fraction of counts assigned to each gene over all cells.
pl.filter_genes_dispersion(result[, log, …])	Plot dispersions versus means for genes.
pl.highly_variable_genes(adata_or_result[, …])	Plot dispersions or normalized variance versus means for genes.

Tools

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.

PCA

pl.pca(adata, *[, color, gene_symbols, …])	Scatter plot in PCA coordinates.
pl.pca_loadings(adata[, components, …])	Rank genes according to contributions to PCs.
pl.pca_variance_ratio(adata[, n_pcs, log, …])	Plot the variance ratio.
pl.pca_overview(adata, **params)	Plot PCA results.

Embeddings

pl.tsne(adata, *[, color, gene_symbols, …])	Scatter plot in tSNE basis.
pl.umap(adata, *[, color, gene_symbols, …])	Scatter plot in UMAP basis.
pl.diffmap(adata, *[, color, gene_symbols, …])	Scatter plot in Diffusion Map basis.
pl.draw_graph(adata, *[, color, …])	Scatter plot in graph-drawing basis.
pl.spatial(adata, *[, color, gene_symbols, …])	Scatter plot in spatial coordinates.
pl.embedding(adata, basis, *[, color, …])	Scatter plot for user specified embedding basis (e.g.

Compute densities on embeddings.

pl.embedding_density(adata[, basis, key, …])

Plot the density of cells in an embedding (per condition).

Branching trajectories and pseudotime, clustering

Visualize clusters using one of the embedding methods passing color='louvain'.

pl.dpt_groups_pseudotime(adata[, color_map, …])	Plot groups and pseudotime.
pl.dpt_timeseries(adata[, color_map, show, …])	Heatmap of pseudotime series.
pl.paga(adata[, threshold, color, layout, …])	Plot the PAGA graph through thresholding low-connectivity edges.
pl.paga_path(adata, nodes, keys[, use_raw, …])	Gene expression and annotation changes along paths in the abstracted graph.
pl.paga_compare(adata[, basis, edges, …])	Scatter and PAGA graph side-by-side.

Marker genes

pl.rank_genes_groups(adata[, groups, …])	Plot ranking of genes.
pl.rank_genes_groups_violin(adata[, groups, …])	Plot ranking of genes for all tested comparisons.
pl.rank_genes_groups_stacked_violin(adata[, …])	Plot ranking of genes using stacked_violin plot (see stacked_violin())
pl.rank_genes_groups_heatmap(adata[, …])	Plot ranking of genes using heatmap plot (see heatmap())
pl.rank_genes_groups_dotplot(adata[, …])	Plot ranking of genes using dotplot plot (see dotplot())
pl.rank_genes_groups_matrixplot(adata[, …])	Plot ranking of genes using matrixplot plot (see matrixplot())
pl.rank_genes_groups_tracksplot(adata[, …])	Plot ranking of genes using heatmap plot (see heatmap())

Simulations

pl.sim(adata[, tmax_realization, …])

Plot results of simulation.

Reading

Note

For reading annotation use pandas.read_… and add it to your anndata.AnnData object. The following read functions are intended for the numeric data in the data matrix X.

Read common file formats using

read(filename[, backed, sheet, ext, …])

Read file and return AnnData object.

Read 10x formatted hdf5 files and directories containing .mtx files using

read_10x_h5(filename[, genome, gex_only, …])	Read 10x-Genomics-formatted hdf5 file.
read_10x_mtx(path[, var_names, make_unique, …])	Read 10x-Genomics-formatted mtx directory.
read_visium(path[, genome, count_file, …])	Read 10x-Genomics-formatted visum dataset.

Read other formats using functions borrowed from anndata

read_h5ad(filename[, backed, as_sparse, …])	Read .h5ad-formatted hdf5 file.
read_csv(filename[, delimiter, …])	Read .csv file.
read_excel(filename, sheet[, dtype])	Read .xlsx (Excel) file.
read_hdf(filename, key)	Read .h5 (hdf5) file.
read_loom(filename, *[, sparse, cleanup, …])	Read .loom-formatted hdf5 file.
read_mtx(filename[, dtype])	Read .mtx file.
read_text(filename[, delimiter, …])	Read .txt, .tab, .data (text) file.
read_umi_tools(filename[, dtype])	Read a gzipped condensed count matrix from umi_tools.

Get object from AnnData: get

The module sc.get provides convenience functions for getting values back in useful formats.

get.obs_df(adata[, keys, obsm_keys, layer, …])	Return values for observations in adata.
get.var_df(adata[, keys, varm_keys, layer])	Return values for observations in adata.
get.rank_genes_groups_df(adata, group, *[, …])	scanpy.tl.rank_genes_groups() results in the form of a DataFrame.

Queries

This module provides useful queries for annotation and enrichment.

queries.biomart_annotations(org, attrs, *[, …])	Retrieve gene annotations from ensembl biomart.
queries.gene_coordinates(org, gene_name, *)	Retrieve gene coordinates for specific organism through BioMart.
queries.mitochondrial_genes(org, *[, …])	Mitochondrial gene symbols for specific organism through BioMart.
queries.enrich() ))	Get enrichment for DE results.

Metrics

Collections of useful measurements for evaluating results.

metrics.confusion_matrix(orig, new[, data, …])	Given an original and new set of labels, create a labelled confusion matrix.
metrics.gearys_c()	Calculate Geary’s C, as used by VISION.
metrics.morans_i()	Calculate Moran’s I Global Autocorrelation Statistic.

Classes

AnnData is reexported from anndata.

Represent data as a neighborhood structure, usually a knn graph.

Neighbors(adata[, n_dcs, neighbors_key])

Data represented as graph of nearest neighbors.

Settings

A convenience function for setting some default matplotlib.rcParams and a high-resolution jupyter display backend useful for use in notebooks.

set_figure_params([scanpy, dpi, dpi_save, …])

Set resolution/size, styling and format of figures.

An instance of the ScanpyConfig is available as scanpy.settings and allows configuring Scanpy.

_settings.ScanpyConfig(*[, verbosity, …])

Config manager for scanpy.

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.

autoshow	Automatically show figures if autosave == False (default True).
autosave	Automatically save figures in figdir (default False).

The default directories for saving figures, caching files and storing datasets.

figdir	Directory for saving figures (default './figures/').
cachedir	Directory for cache files (default './cache/').
datasetdir	Directory for example datasets (default './data/').

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.

verbosity

Verbosity level (default warning)

Print versions of packages that might influence numerical results.

logging.print_header(*[, file])	Versions that might influence the numerical results.
logging.print_versions(*[, file])	Print print versions of imported packages

Datasets

datasets.blobs([n_variables, n_centers, …])	Gaussian Blobs.
datasets.ebi_expression_atlas(accession, *)	Load a dataset from the EBI Single Cell Expression Atlas
datasets.krumsiek11()	Simulated myeloid progenitors [Krumsiek11].
datasets.moignard15()	Hematopoiesis in early mouse embryos [Moignard15].
datasets.pbmc3k()	3k PBMCs from 10x Genomics.
datasets.pbmc3k_processed()	Processed 3k PBMCs from 10x Genomics.
datasets.pbmc68k_reduced()	Subsampled and processed 68k PBMCs.
datasets.paul15()	Development of Myeloid Progenitors [Paul15].
datasets.toggleswitch()	Simulated toggleswitch.
datasets.visium_sge([sample_id, …])	Processed Visium Spatial Gene Expression data from 10x Genomics.

Deprecated functions

pp.filter_genes_dispersion(data[, flavor, …])	Extract highly variable genes [Satija15] [Zheng17].
pp.normalize_per_cell(data[, …])	Normalize total counts per cell.