do_spatial_knn_smoothing: do_spatial_knn_smoothing

In RubD/Giotto: Spatial Single-Cell Transcriptomics Toolbox

do_spatial_knn_smoothing

Description

smooth gene expression over a kNN spatial network

Usage

do_spatial_knn_smoothing(
  gobject,
  expression_values = c("normalized", "scaled", "custom"),
  subset_genes = NULL,
  spatial_network_name = "Delaunay_network",
  b = NULL
)

Arguments

gobject	giotto object
expression_values	gene expression values to use
subset_genes	subset of genes to use
spatial_network_name	name of spatial network to use
b	smoothing factor beteen 0 and 1 (default: automatic)

Details

This function will smoothen the gene expression values per cell according to its neighbors in the selected spatial network.
b is a smoothening factor that defaults to 1 - 1/k, where k is the median number of k-neighbors in the selected spatial network. Setting b = 0 means no smoothing and b = 1 means no contribution from its own expression.

Value

matrix with smoothened gene expression values based on kNN spatial network

RubD/Giotto documentation built on April 29, 2023, 5:52 p.m.