plotting.md

Plotting: pl

.. 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 {doc}/tutorials/plotting/core for an overview of how to use these functions.

See the {ref}`settings` section for all important plotting configurations.

(pl-generic)=

Generic

.. autosummary::
   :nosignatures:
   :toctree: ../generated/

   pl.scatter
   pl.heatmap
   pl.dotplot
   pl.tracksplot
   pl.violin
   pl.stacked_violin
   pl.matrixplot
   pl.clustermap
   pl.ranking
   pl.dendrogram

Classes

These classes allow fine tuning of visual parameters.

.. autosummary::
   :nosignatures:
   :toctree: generated/classes

    pl.DotPlot
    pl.MatrixPlot
    pl.StackedViolin

Preprocessing

Methods for visualizing quality control and results of preprocessing functions.

.. autosummary::
   :nosignatures:
   :toctree: generated/

   pl.highest_expr_genes
   pl.filter_genes_dispersion
   pl.highly_variable_genes
   pl.scrublet_score_distribution

Tools

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.

PCA

.. autosummary::
   :nosignatures:
   :toctree: generated/

   pl.pca
   pl.pca_loadings
   pl.pca_variance_ratio
   pl.pca_overview

(pl-embeddings)=

Embeddings

.. autosummary::
   :nosignatures:
   :toctree: generated/

   pl.tsne
   pl.umap
   pl.diffmap
   pl.draw_graph
   pl.spatial
   pl.embedding

Compute densities on embeddings.

.. autosummary::
   :nosignatures:
   :toctree: generated/

   pl.embedding_density

Branching trajectories and pseudotime, clustering

Visualize clusters using one of the embedding methods passing e.g. color='leiden'.

.. autosummary::
   :nosignatures:
   :toctree: generated/

   pl.dpt_groups_pseudotime
   pl.dpt_timeseries
   pl.paga
   pl.paga_path
   pl.paga_compare

Marker genes

.. autosummary::
   :nosignatures:
   :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

Simulations

.. autosummary::
   :nosignatures:
   :toctree: generated/

   pl.sim