ModuleNetworkPlot: ModuleNetworkPlot
In smorabit/hdWGCNA: hdWGCNA

ModuleNetworkPlot

R Documentation

ModuleNetworkPlot

Description

Visualizes the top hub genes for selected modules as a circular network plot with one inner circle and one outer circle.

Usage

ModuleNetworkPlot(
  seurat_obj,
  n_inner = 10,
  n_outer = 15,
  n_conns = 500,
  mods = "all",
  outdir = "ModuleNetworks",
  wgcna_name = NULL,
  plot_size = c(6, 6),
  edge.alpha = 0.25,
  edge.width = 1,
  vertex.label.cex = 1,
  vertex.size = 6,
  ...
)

Arguments

`seurat_obj`	A Seurat object
`n_inner`	Number of genes to plot on the inner circle
`n_outer`	Number of genes to plot on the outer circle.
`n_conns`	Number of gene-gene co-expression connections to plot, sorted by the strongest connections.
`mods`	Names of the modules to plot. If mods = "all", all modules are plotted.
`outdir`	The directory where the plots will be stored.
`wgcna_name`	The name of the hdWGCNA experiment in the seurat_obj@misc slot
`plot_size`	A vector containing the width and height of the network plots. example: c(5,5)
`edge.alpha`	value between 0 and 1 determining the alpha (transparency) scaling factor for the network edges
`edge.width`	value determining the width of the network edges
`vertex.label.cex`	vertex label font size
`vertex.size`	vertex size