GetSpatNet: Create Spatial Networks

In jbergenstrahle/STUtility: Analysis and visualization of Spatial Transcriptomics data

Create Spatial Networks

Description

Create spatial networks based on spot center to center distances from a Seurat object.

Usage

GetSpatNet(object, nNeighbours = NULL, maxdist = NULL, minK = 0)

Arguments

object	Seurat object
nNeighbours	Number of nearest neighbours to calculate for each spot. The default number of neighbours is 6 for the 'Visium' platform and 4 for the '1k' and '2k' platforms.
maxdist	Distance cut-off for nearest neighbours to consider. The default is 1.5 for the 'Visium' and '2k' platforms and 2 for the '1k' platform.
minK	Minimum nearest neigbhours if maxdist is not provided [default: 0]

Examples

## Not run: 
spatial.networks <- GetSpatNet(se)

## End(Not run)

jbergenstrahle/STUtility documentation built on March 14, 2023, 7:15 a.m.