detectSpatialCorGenes: detectSpatialCorGenes

In drieslab/Giotto_site_suite: Spatial Single-Cell Transcriptomics Toolbox

detectSpatialCorGenes

Description

Detect genes that are spatially correlated

Usage

detectSpatialCorGenes(
  gobject,
  feat_type = NULL,
  spat_unit = NULL,
  method = c("grid", "network"),
  expression_values = c("normalized", "scaled", "custom"),
  subset_feats = NULL,
  subset_genes = NULL,
  spatial_network_name = "Delaunay_network",
  network_smoothing = NULL,
  spatial_grid_name = "spatial_grid",
  min_cells_per_grid = 4,
  cor_method = c("pearson", "kendall", "spearman")
)

Arguments

gobject	giotto object
feat_type	feature type
spat_unit	spatial unit
method	method to use for spatial averaging
expression_values	gene expression values to use
subset_feats	subset of feats to use
subset_genes	deprecated, use subset_feats
spatial_network_name	name of spatial network to use
network_smoothing	smoothing factor beteen 0 and 1 (default: automatic)
spatial_grid_name	name of spatial grid to use
min_cells_per_grid	minimum number of cells to consider a grid
cor_method	correlation method

Details

For method = network, it expects a fully connected spatial network. You can make sure to create a fully connected network by setting minimal_k > 0 in the createSpatialNetwork function.

• 1. grid-averaging: average gene expression values within a predefined spatial grid

• 2. network-averaging: smoothens the gene expression matrix by averaging the expression within one cell by using the neighbours within the predefined 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.

The spatCorObject can be further explored with showSpatialCorGenes()

Value

returns a spatial correlation object: "spatCorObject"

See Also

showSpatialCorGenes

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