plot_networks: Plot correlation networks

In mselensky/bngal: Biological Network Graphing and Learning

Plot correlation networks

Description

Plot correlation networks

Usage

plot_networks(
  node.color.data,
  filled.by,
  graph.layout,
  out.dr,
  sign,
  direction,
  cutoff.val,
  pval.cutoff,
  other.variable
)

Arguments

node.color.data	Output from color_nodes()
filled.by	Value by which to color network nodes. Also defines the drop-down option for interactive network plot. Values of 'phylum', 'edge_btwn_cluster', or 'other' accepted. If 'other' is chosen, the desired custom color scheme must be saved as a column labeled hex.color (containing hex codes) in node.color.data[[nodes]]
graph.layout	igraph-style layout option for interactive network plot. Refer to the igraph documentation for the full list of options. See also visNetwork::visIgraphLayout()
out.dr	Figure output directory (does not have to exist in parent directory)
sign	Optional See prepro_net_features(). For plot/output file name, if desired.
direction	Optional See prepare_network_data(). For plot/output file name, if desired.
cutoff.val	Optional See prepare_network_data(). For plot/output file name, if desired.
pval.cutoff	Optional See prepro_net_features(). For plot/output file name, if desired.
other.variable	Optional Only required if filled.by == 'other'. Name of nodes column by which to select node groupings.

mselensky/bngal documentation built on June 3, 2024, 6:27 a.m.