api.rst

.. module:: stlearn

.. automodule:: stlearn
   :noindex:

API

Import stLearn as:

import stlearn as st

Wrapper functions: wrapper

.. module:: stlearn.wrapper

.. currentmodule:: stlearn

.. autosummary::
   :toctree: .

   Read10X
   ReadOldST
   ReadSlideSeq
   ReadMERFISH
   ReadSeqFish
   convert_scanpy
   create_stlearn

Add: add

.. module:: stlearn.add

.. currentmodule:: stlearn

.. autosummary::
   :toctree: .

   add.image
   add.positions
   add.parsing
   add.lr
   add.labels
   add.annotation
   add.add_loupe_clusters
   add.add_mask
   add.apply_mask
   add.add_deconvolution

Preprocessing: pp

.. module:: stlearn.pp

.. currentmodule:: stlearn

.. autosummary::
   :toctree: .

   pp.filter_genes
   pp.log1p
   pp.normalize_total
   pp.scale
   pp.neighbors
   pp.tiling
   pp.extract_feature

Embedding: em

.. module:: stlearn.em

.. currentmodule:: stlearn

.. autosummary::
   :toctree: .

   em.run_pca
   em.run_umap
   em.run_ica
   em.run_fa
   em.run_diffmap

Spatial: spatial

.. module:: stlearn.spatial.clustering

.. currentmodule:: stlearn

.. autosummary::
   :toctree: .

   spatial.clustering.localization

.. module:: stlearn.spatial.trajectory

.. currentmodule:: stlearn

.. autosummary::
   :toctree: .

   spatial.trajectory.pseudotime
   spatial.trajectory.pseudotimespace_global
   spatial.trajectory.pseudotimespace_local
   spatial.trajectory.compare_transitions
   spatial.trajectory.detect_transition_markers_clades
   spatial.trajectory.detect_transition_markers_branches

.. module:: stlearn.spatial.morphology

.. currentmodule:: stlearn

.. autosummary::
   :toctree: .

   spatial.morphology.adjust

.. module:: stlearn.spatial.SME

.. currentmodule:: stlearn

.. autosummary::
   :toctree: .

   spatial.SME.SME_impute0
   spatial.SME.pseudo_spot
   spatial.SME.SME_normalize

Tools: tl

.. module:: stlearn.tl.clustering

.. currentmodule:: stlearn

.. autosummary::
   :toctree: .

   tl.clustering.kmeans
   tl.clustering.louvain

.. module:: stlearn.tl.cci

.. currentmodule:: stlearn

.. autosummary::
   :toctree: .

   tl.cci.load_lrs
   tl.cci.grid
   tl.cci.run
   tl.cci.adj_pvals
   tl.cci.run_lr_go
   tl.cci.run_cci

Plot: pl

.. module:: stlearn.pl

.. currentmodule:: stlearn

.. autosummary::
   :toctree: .

   pl.QC_plot
   pl.gene_plot
   pl.gene_plot_interactive
   pl.cluster_plot
   pl.cluster_plot_interactive
   pl.subcluster_plot
   pl.subcluster_plot
   pl.non_spatial_plot
   pl.deconvolution_plot
   pl.plot_mask
   pl.lr_summary
   pl.lr_diagnostics
   pl.lr_n_spots
   pl.lr_go
   pl.lr_result_plot
   pl.lr_plot
   pl.cci_check
   pl.ccinet_plot
   pl.lr_chord_plot
   pl.lr_cci_map
   pl.cci_map
   pl.lr_plot_interactive
   pl.spatialcci_plot_interactive

.. module:: stlearn.pl.trajectory

.. currentmodule:: stlearn

.. autosummary::
   :toctree: .

   pl.trajectory.pseudotime_plot
   pl.trajectory.local_plot
   pl.trajectory.tree_plot
   pl.trajectory.transition_markers_plot
   pl.trajectory.DE_transition_plot

Tools: datasets

.. module:: stlearn.datasets

.. currentmodule:: stlearn

.. autosummary::
   :toctree: .

   datasets.example_bcba()