API Reference#

Config#

Global configurations for spatialtis.

Read single cell data from images and masks.

Read visium data from visium result folders.

`wkt_points`	Transform normal coordination in AnnData.obs to wkt-format.
`wkt_shapes`	Transform normal coordination in AnnData.obs to wkt-format.

Read spatialtis result from AnnData.uns as pandas.DataFrame object.

`cell_components`	Count the proportion of each types of cells in each group.
`cell_density`	Calculating cell density in each ROI.
`cell_morphology`	Cell morphology variation between different groups.
`cell_co_occurrence`	The likelihood of two type of cells occur simultaneously in a ROI.

`find_neighbors`	To find the neighbors of each cell.
`spatial_weights`	A generator that return spatial weight in CSR matrix
`hotspot`	Getis-ord hotspot detection
`cell_dispersion`	Cell distribution pattern
`cell_interaction`	Profiling cell-cell interaction using permutation test
`cell_community`	Spatial communities detection
`spatial_heterogeneity`	Evaluate tissue heterogeneity based on entropy
`spatial_autocorr`	Spatial auto-correlation for every marker.
`spatial_enrichment`	Profiling markers spatial enrichment using permutation test
`spatial_coexp`	Identifying spatial co-expression markers using correlation
`NCD_marker`	Identify neighbor cells dependent marker
`NMD_marker`	Identify neighbor markers dependent marker
`somde`	This is a wrapper around somde
`GCNG`	A pytorch reimplementation of GCNG

The base class for all analysis function

To use plotting, import it in following schema:

>>> import spatialtis.plotting as sp

`plotting.cell_map`	Visualize cells and neighbors relationship in ROI
`plotting.expression_map`	Visualize marker expression in ROI

`plotting.cell_components`	Visualization of the cell components
`plotting.cell_density`	Visualization of cell density
`plotting.cell_morphology`	Visualization of cell morphology
`plotting.cell_co_occurrence`	Visualization of cell co-occurrence
`plotting.cell_dispersion`	Parameters
`plotting.spatial_heterogeneity`	Visualization of spatial heterogeneity analysis
`plotting.cell_interaction`	Visualization of the cell interaction analysis
`plotting.spatial_enrichment`	Visualization of the spatial enrichment analysis