createNearestNetwork: createNearestNetwork

In drieslab/Giotto_site_suite: Spatial Single-Cell Transcriptomics Toolbox

createNearestNetwork

Description

create a nearest neighbour (NN) network

Usage

createNearestNetwork(
  gobject,
  spat_unit = NULL,
  feat_type = NULL,
  type = c("sNN", "kNN"),
  dim_reduction_to_use = "pca",
  dim_reduction_name = NULL,
  dimensions_to_use = 1:10,
  feats_to_use = NULL,
  genes_to_use = NULL,
  expression_values = c("normalized", "scaled", "custom"),
  name = NULL,
  return_gobject = TRUE,
  k = 30,
  minimum_shared = 5,
  top_shared = 3,
  verbose = T,
  ...
)

Arguments

gobject	giotto object
spat_unit	spatial unit (e.g. "cell")
feat_type	feature type (e.g. "rna", "dna", "protein")
type	sNN or kNN
dim_reduction_to_use	dimension reduction method to use
dim_reduction_name	name of dimension reduction set to use
dimensions_to_use	number of dimensions to use as input
feats_to_use	if dim_reduction_to_use = NULL, which genes to use
genes_to_use	deprecated, use feats_to_use
expression_values	expression values to use
name	arbitrary name for NN network. Defaults to [type].[dim_reduction_to_use]
return_gobject	boolean: return giotto object (default = TRUE)
k	number of k neighbors to use
minimum_shared	minimum shared neighbors
top_shared	keep at ...
verbose	be verbose
...	additional parameters for kNN and sNN functions from dbscan

Details

This function creates a k-nearest neighbour (kNN) or shared nearest neighbour (sNN) network based on the provided dimension reduction space. To run it directly on the gene expression matrix set dim_reduction_to_use = NULL.

See also kNN and sNN for more information about how the networks are created.

Output for kNN:

• from: cell_ID for source cell

• to: cell_ID for target cell

• distance: distance between cells

• weight: weight = 1/(1 + distance)

Output for sNN:

• from: cell_ID for source cell

• to: cell_ID for target cell

• distance: distance between cells

• weight: 1/(1 + distance)

• shared: number of shared neighbours

• rank: ranking of pairwise cell neighbours

For sNN networks two additional parameters can be set:

• minimum_shared: minimum number of shared neighbours needed

• top_shared: keep this number of the top shared neighbours, irrespective of minimum_shared setting

Value

giotto object with updated NN network

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