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