addNetworkLayout#

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Last Updated: Mar 11, 2023

Description#

Add a network layout for a selected nearest neighbor network

Usage#

addNetworkLayout(
  gobject,
  spat_unit = NULL,
  feat_type = NULL,
  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

spat_unit

spatial unit

feat_type

feature type

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)

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.

Value#

giotto object with updated layout for selected NN network