api.md

API

.. module:: squidpy

Import Squidpy as:

import squidpy as sq

Graph

.. module:: squidpy.gr
.. currentmodule:: squidpy
.. autosummary::
    :toctree: api

    gr.spatial_neighbors
    gr.spatial_neighbors_from_builder
    gr.spatial_neighbors_knn
    gr.spatial_neighbors_radius
    gr.spatial_neighbors_delaunay
    gr.spatial_neighbors_grid
    gr.GraphMatrixT
    gr.SpatialNeighborsResult
    gr.mask_graph
    gr.nhood_enrichment
    gr.NhoodEnrichmentResult
    gr.co_occurrence
    gr.centrality_scores
    gr.interaction_matrix
    gr.ripley
    gr.ligrec
    gr.spatial_autocorr
    gr.sepal

Image

.. module:: squidpy.im
.. currentmodule:: squidpy
.. autosummary::
    :toctree: api

    im.process
    im.segment
    im.calculate_image_features
    im.SegmentationModel

Plotting

.. module:: squidpy.pl
.. currentmodule:: squidpy
.. autosummary::
    :toctree: api

    pl.spatial_scatter
    pl.spatial_segment
    pl.nhood_enrichment
    pl.centrality_scores
    pl.interaction_matrix
    pl.ligrec
    pl.ripley
    pl.co_occurrence
    pl.extract
    pl.var_by_distance

Reading

.. module:: squidpy.read
.. currentmodule:: squidpy
.. autosummary::
    :toctree: api

    read.visium
    read.vizgen
    read.nanostring

Tools

.. module:: squidpy.tl
.. currentmodule:: squidpy
.. autosummary::
    :toctree: api

    tl.sliding_window
    tl.var_by_distance

Datasets

.. module:: squidpy.datasets
.. currentmodule:: squidpy
.. autosummary::
    :toctree: api

    datasets.four_i
    datasets.imc
    datasets.seqfish
    datasets.merfish
    datasets.mibitof
    datasets.slideseqv2
    datasets.sc_mouse_cortex
    datasets.visium
    datasets.visium_hne_adata
    datasets.visium_hne_adata_crop
    datasets.visium_fluo_adata
    datasets.visium_fluo_adata_crop
    datasets.visium_hne_image
    datasets.visium_hne_image_crop
    datasets.visium_fluo_image_crop

Extensibility

See the {doc}extensibility guide </extensibility> for how to implement a custom graph builder.

.. module:: squidpy.gr.neighbors
.. currentmodule:: squidpy
.. autosummary::
    :toctree: api

    gr.neighbors.GraphBuilder
    gr.neighbors.GraphBuilderCSR
    gr.neighbors.GraphMatrixT
    gr.neighbors.GraphPostprocessor
    gr.neighbors.DistanceIntervalPostprocessor
    gr.neighbors.PercentilePostprocessor
    gr.neighbors.TransformPostprocessor
    gr.neighbors.KNNBuilder
    gr.neighbors.RadiusBuilder
    gr.neighbors.DelaunayBuilder
    gr.neighbors.GridBuilder