do_spatial_knn_smoothing: do_spatial_knn_smoothing
In bernard2012/Giotto: Spatial single-cell transcriptomics toolbox

Description Usage Arguments Details Value Examples

smooth gene expression over a kNN spatial network

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

`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)

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.

matrix with smoothened gene expression values based on kNN spatial network