do_spatial_knn_smoothing: do_spatial_knn_smoothing

In drieslab/Giotto_site_suite: Spatial Single-Cell Transcriptomics Toolbox

do_spatial_knn_smoothing

Description

smooth gene expression over a kNN spatial network

Usage

do_spatial_knn_smoothing(
  expression_matrix,
  spatial_network,
  subset_feats = NULL,
  b = NULL
)

Arguments

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

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

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