# Scanpy – Single-Cell Analysis in Python¶

Scanpy is a scalable toolkit for analyzing single-cell gene expression data built jointly with anndata. It includes preprocessing, visualization, clustering, trajectory inference and differential expression testing. The Python-based implementation efficiently deals with datasets of more than one million cells.

## News¶

### COVID-19 datasets distributed as h5ad2020-04-01¶

In a joint initiative, the Wellcome Sanger Institute, the Human Cell Atlas, and the CZI distribute datasets related to COVID-19 via anndata’s h5ad files: covid19cellatlas.org. It wasn’t anticipated that the initial idea of sharing and backing an on-disk representation of AnnData would become so widely adopted. Curious? Read up more on the format.

### CZI grant 2019-11-14¶

Scanpy has been selected an essential open source software for science by CZI among 32 projects, along with giants such as Scipy, Numpy, Pandas, Matplotlib, scikit-learn, scikit-image/plotly, pip, jupyterhub/binder, Bioconda, Seurat, Bioconductor, and others.

### 1.6.0 2020-08-15¶

This release includes an overhaul of dotplot(), matrixplot(), and stacked_violin() (PR 1210 F Ramirez), and of the internals of rank_genes_groups() (PR 1156 S Rybakov).

Overhaul of dotplot(), matrixplot(), and stacked_violin() PR 1210 F Ramirez

• An overhauled tutorial → tutorial: plotting/core.

• New plotting classes can be accessed directly (e.g., DotPlot) or using the return_fig param.

• It is possible to plot log fold change and p-values in the rank_genes_groups_dotplot() family of functions.

• Added ax parameter which allows embedding the plot in other images.

• Added option to include a bar plot instead of the dendrogram containing the cell/observation totals per category.

• Return a dictionary of axes for further manipulation. This includes the main plot, legend and dendrogram to totals

• Legends can be removed.

• The groupby param can take a list of categories, e.g., groupby=[‘tissue’, ‘cell type’].

• Added padding parameter to dotplot and stacked_violin. PR 1270

• Added title for colorbar and positioned as in dotplot for matrixplot().

• dotplot() changes:

• Improved the colorbar and size legend for dotplots. Now the colorbar and size have titles, which can be modified using the colorbar_title and size_title params. They also align at the bottom of the image and do not shrink if the dotplot image is smaller.

• Allow plotting genes in rows and categories in columns (swap_axes).

• Using DotPlot, the dot_edge_color and line width can be modified, a grid can be added, and other modifications are enabled.

• A new style was added in which the dots are replaced by an empty circle and the square behind the circle is colored (like in matrixplots).

• stacked_violin() changes:

• Violin colors can be colored based on average gene expression as in dotplots.

• The linewidth of the violin plots is thinner.

• Removed the tics for the y-axis as they tend to overlap with each other. Using the style method they can be displayed if needed.