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Introduction:

  • Introduction

Getting started

  • Installation
  • Tutorial 1: Data handling
  • Tutorial 2: Pixel map integration
  • Tutorial 3: Scanpy and AnnData integration
  • Tutorial 4: Exploratory analysis
  • Tutorial 5: Statistical modeling

User guide:

  • The SpatialData object:
  • The PixelMap object
  • The SpatialStatistics object
  • Next Neighbor analysis and spatial contexts:
  • Integrating scanpy/Anndata

Modules:

  • plankton
plankton.py
  • »
  • Index
  • Edit on GitHub

Index

C | D | G | K | M | N | P | R | S | U

C

  • co_occurrence() (in module plankton.stats)

D

  • distances (plankton.graph.SpatialGraph property)

G

  • get_histograms() (in module plankton.stats)

K

  • knn_entropy() (plankton.graph.SpatialGraph method)

M

  • map_and_umap() (plankton.graph.SpatialGraph method)
  • module
    • plankton
    • plankton.graph
    • plankton.stats
  • mor_normalize() (in module plankton.stats)

N

  • neighbor_types (plankton.graph.SpatialGraph property)
  • neighbors (plankton.graph.SpatialGraph property)

P

  • plankton
    • module
  • plankton.graph
    • module
  • plankton.stats
    • module
  • plot_entropy() (plankton.graph.SpatialGraph method)
  • plot_umap() (plankton.graph.SpatialGraph method)

R

  • ripleys_k() (in module plankton.stats)
  • run_umap() (plankton.graph.SpatialGraph method)

S

  • SpatialGraph (class in plankton.graph)

U

  • umap (plankton.graph.SpatialGraph property)
  • umap_0 (plankton.graph.SpatialGraph property)
  • umap_1 (plankton.graph.SpatialGraph property)
  • umap_js() (plankton.graph.SpatialGraph method)
  • update_knn() (plankton.graph.SpatialGraph method)

© Copyright 2022, Sebastian Tiesmeyer. Revision 1bae350e.

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