addNetworkLayout: addNetworkLayout

In bernard2012/Giotto: Spatial single-cell transcriptomics toolbox

Description

Add a network layout for a selected nearest neighbor network

Usage

addNetworkLayout(
  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)

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

Examples

    addNetworkLayout(gobject)

bernard2012/Giotto documentation built on Sept. 22, 2020, 10:29 a.m.