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Usage Principles

Import Scanpy as:

import scanpy as sc


The typical workflow consists of subsequent calls of data analysis tools in, e.g.:, **tool_params)  # embed the data using tSNE

where adata is an :class:`~anndata.AnnData` object. Each of these calls adds annotation to an expression matrix X, which stores n_obs observations (cells) of n_vars variables (genes). For each tool, there typically is an associated plotting function in, **plotting_params)

If you pass show=False, a :class:`matplotlib.axes.Axes` instance is returned and you have all of matplotlib's detailed configuration possibilities.

To facilitate writing memory-efficient pipelines, by default, Scanpy tools operate inplace on adata and return None - this also allows to easily transition to out-of-memory pipelines. If you want to return a copy of the :class:`~anndata.AnnData` object and leave the passed adata unchanged, pass copy=True.


Scanpy is based on :mod:`anndata`, which provides the :class:`~anndata.AnnData` class.

At the most basic level, an :class:`~anndata.AnnData` object adata stores a data matrix (adata.X), dataframe-like annotation of observations (adata.obs) and variables (adata.var) and unstructured dict-like annotation (adata.uns). Values can be retrieved and appended via adata.obs['key1'] and adata.var['key2']. Names of observations and variables can be accessed via adata.obs_names and adata.var_names, respectively. :class:`~anndata.AnnData` objects can be sliced like dataframes, for example, adata_subset = adata[:, list_of_gene_names]. For more, see this blog post.

To read a data file to an :class:`~anndata.AnnData` object, call:

adata =

to initialize an :class:`~anndata.AnnData` object. Possibly add further annotation using, e.g., pd.read_csv:

import pandas as pd
anno = pd.read_csv(filename_sample_annotation)
adata.obs['cell_groups'] = anno['cell_groups']  # categorical annotation of type pandas.Categorical
adata.obs['time'] = anno['time']                # numerical annotation of type float
# alternatively, you could also set the whole dataframe
# adata.obs = anno

To write, use: