Create Giotto Visium Object

createNearestNetwork()

Create a nearest neighbor (NN) network.

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

Arguments

gobject	giotto object
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
genes_to_use	if dim_reduction_to_use = NULL, which genes to use
expression_values	expression values to use
name	arbitrary name for NN network
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

Value

Giotto object with updated NN network

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

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

Output for kNN:	Output for sNN:
to: cell_ID for target cell	to: cell_ID for target cell
distance: distance between cells	distance: distance between cells
weight: weight = 1/(1 + distance)	weight: 1/(1 + distance)
	shared: number of shared neighbors
	rank: ranking of pairwise cell neighbors

Note

For sNN networks two additional parameters can be set:

1. minimum_shared: minimum number of shared neighbors needed

2. top_shared: keep this number of the top shared neighbors, irrespective of minimum_shared setting

Examples

data(mini_giotto_single_cell)

mini_giotto_single_cell <- createNearestNetwork(gobject = mini_giotto_single_cell,
                    dimensions_to_use = 1:3, k = 3)
#>
#>   sNN.pca  has already been used, will be overwritten