createSpatialWeightMatrix: Create a spatial weight matrix

In drieslab/Giotto_site_suite: Spatial Single-Cell Transcriptomics Toolbox

Create a spatial weight matrix

Description

Generate spatial weight matrix based on the strength of spatial interactions between nodes. Requires spatial networks to be first generated.

Usage

createSpatialWeightMatrix(
  gobject,
  spat_unit = NULL,
  spatial_network_to_use = "kNN_network",
  method = c("distance", "adjacency"),
  wm_name = "spat_weights",
  return_gobject = TRUE,
  verbose = TRUE
)

Arguments

gobject	giotto object
spat_unit	spatial unit
spatial_network_to_use	spatial network information to use
method	type of weighted matrix to generate. See details
wm_name	name to assign the weight matrix values
return_gobject	(default = TRUE) whether to return as the giotto object with attached results or the bare weighted matrix
verbose	be verbose

Details

• "distance" method is calculated using 1/(1+distance) to create an inverse weighting based on the distance between nodes.

• "adjacency" method is a binary matrix with 1 signifying that two nodes are connected in the spatial network and 0 indicating that they are not.

drieslab/Giotto_site_suite documentation built on April 26, 2023, 11:51 p.m.