createSpatialKNNnetwork#

Date

2022-10-06

https://github.com/drieslab/Giotto/tree/suite/R/spatial_structures.R#L1420

Description#

Create a spatial knn network.

Usage#

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

Arguments#

Argument

Description

gobject

giotto object

method

method to create kNN network

spat_unit

spatial unit

feat_type

feature type

spat_loc_name

name of spatial locations

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)

list()

additional arguments to the selected method function

Value#

giotto object with updated spatial network slot

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