Add Network Layout

addNetworkLayout()

Add a network layout for a selected nearest neighbor network.

caddNetworkLayout(
    gobject,
    nn_network_to_use = "sNN",
    network_name = "sNN.pca",
    layout_type = c("drl"),
    options_list = NULL,
    layout_name = "layout",
    return_gobject = TRUE
)

Arguments

gobject	giotto object
nn_network_to_use	kNN or sNN
network_name	name of NN network to be used
layout_type	layout algorithm to use
options_list	list of options for selected layout
layout_name	name for layout
return_gobject	boolean: return giotto object (default = TRUE)

Value

Giotto object with updated layout for selected NN network

Details

This function creates layout coordinates based on the provided kNN or sNN. Currently only the force-directed graph layout “drl”, see layout_with_drl, is implemented. This provides an alternative to tSNE or UMAP based visualizations.