scW.p.network: Plots a fruchtermanreingold network of the co-expression...

In CFeregrino/scWGCNA: WGCNA Analyses on Single-cell Data

Plots a fruchtermanreingold network of the co-expression modules.

Description

This function will help us plot a fruchtermanreingold network of each of the co-expression modules calculated by scWGCNA.

Usage

scW.p.network(scWGCNA.data, module = 1, gnames = NULL, ...)

Arguments

scWGCNA.data	scWGCNA.data. An scWGCNA.data object, as calculated by run.scWGCNA().
module	numeric . Which module should be plotted?
gnames	Data frame. If you're using gene IDs and no symbols, you might wanna provide a list of gene names for plotting. Two columns: 1= ids present in expression matrix, 2= names to appear in plots. Rownames= same as 1st row
...	Parameters passed to GGally::ggnet2()

Value

A plot showing the relationships between the genes in a module. The layot represents a fruchtermanreingold network. The size of the nodes represent the relative membership of the gene, to the module. The size of the edges represent the relative topology overlap between two genes.

Examples

# Calculate the networks in the scWCGNA object
MmLimbE155.scWGCNA = scWGCNA.networks(MmLimbE155.scWGCNA)

# Plot one of the modules as network
scW.p.network(MmLimbE155.scWGCNA, module=1)

# If you're using IDs instead of names, and have a separate gene names data.frame
scW.p.network(MmLimbE155.scWGCNA, module=1, gnames = my.small_MmLimbE155@misc$gnames)

CFeregrino/scWGCNA documentation built on Nov. 21, 2022, 2:31 a.m.