ModuleNetworkPlot

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

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