get_network_graph: Compute network graph embedding using UMAP.

In quadbiolab/Pando: Inferring regulomes from multi-modal single-cell genomics data

Compute network graph embedding using UMAP.

Description

Compute network graph embedding using UMAP.

Usage

get_network_graph(object, ...)

## S3 method for class 'GRNData'
get_network_graph(
  object,
  network = DefaultNetwork(object),
  graph_name = "module_graph",
  rna_assay = "RNA",
  rna_layer = "data",
  umap_method = c("weighted", "corr", "coef", "none"),
  features = NULL,
  random_seed = 111,
  verbose = TRUE,
  ...
)

Arguments

object	An object.
...	Additional arguments for uwot.
network	Name of the network to use.
graph_name	Name of the graph.
rna_assay	Name of the RNA assay.
rna_layer	Name of the RNA slot to use.
umap_method	Method to compute edge weights for UMAP: 'weighted' - Correlation weighted by GRN coefficient. 'corr' - Only correlation. 'coef' - Only GRN coefficient. 'none' - Don't compute UMAP and create the graph directly from modules.
features	Features to use to create the graph. If NULL uses all features in the network.
random_seed	Random seed for UMAP computation
verbose	Print messages.

Value

A GRNData object.

quadbiolab/Pando documentation built on April 22, 2024, 8:14 a.m.