Create Spatial KNN Network

createSpatialKNNnetwork()

Create a spatial knn network.

createSpatialKNNnetwork(
    gobject,
    method = "dbscan",
    dimensions = "all",
    name = "knn_network",
    k = 4,
    maximum_distance = NULL,
    minimum_k = 0,
    verbose = F,
    return_gobject = TRUE,
    ...
)

Arguments

gobject	giotto object
method	method to create kNN network
dimensions	which spatial dimensions to use (default = all)
name	name for spatial network (default = ‘spatial_network’)
k	number of nearest neighbors based on physical distance
maximum_distance	distance cuttof for nearest neighbors to consider for kNN network
minimum_k	minimum nearest neigbhours if maximum_distance != NULL
verbose	verbose
return_gobject	boolean: return giotto object (default = TRUE)
…	additional arguments to the selected method function

Value

A Giotto object with updated spatial network slot.

Details

dimensions: default = ‘all’ which takes all possible dimensions. Alternatively you can provide a character vector that specififies the spatial dimensions to use, e.g. c(“sdimx’, “sdimy”) or a numerical vector, e.g. 2:3

maximum_distance: to create a network based on maximum distance only, you also need to set k to a very high value, e.g. k = 100