createSpatialFeaturesKNNnetwork: Create kNN spatial feature network

In drieslab/Giotto_site_suite: Spatial Single-Cell Transcriptomics Toolbox

Create kNN spatial feature network

Description

Calculates the centroid locations for the giotto polygons

Usage

createSpatialFeaturesKNNnetwork(
  gobject,
  method = c("dbscan"),
  feat_type = NULL,
  name = "knn_feats_network",
  k = 4,
  maximum_distance = NULL,
  minimum_k = 0,
  add_feat_ids = FALSE,
  verbose = TRUE,
  return_gobject = TRUE,
  toplevel_params = 2,
  ...
)

Arguments

gobject	giotto object
method	kNN algorithm method
feat_type	feature type to build feature network
name	name of network
k	number of neighbors
maximum_distance	maximum distance bewteen features
minimum_k	minimum number of neighbors to find
add_feat_ids	add feature id names (default = FALSE, increases object size)
verbose	be verbose
return_gobject	return giotto object (default: TRUE)
toplevel_params	toplevel value to pass when updating giotto params
...	additional parameters to pass to kNN

Value

If return_gobject = TRUE a giotto object containing the network will be returned. If return_gobject = FALSE the network will be returned as a datatable.

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