wgcna2igraph: Generate an igraph object from wgcna output

In jtlovell/RNAseqDE: A pipeline for differential expression analyses in R

Description

wgcna2igraph Function to cull and plot WGCNA networks. Requires igraph and WGCNA to be installed.

Usage

wgcna2igraph(net, datExpr, top.n.edges = NA, modules2plot = NULL,
  colors2plot = NULL, kME.threshold = 0.75, adjacency.threshold = 0.1,
  adj.power = 6, verbose = T, min.edge = 2, node.size = 0,
  frame.color = NA, node.color = NA, edge.alpha = 0.5, edge.width = 1,
  returnNet = TRUE, ...)

Arguments

net	WGCNA generated network. Usually from WGCNA::blockwiseModules
datExpr	The expression dataset, transposed so that genes are columns and individuals are rows.
modules2plot	The names (usually colors) of the WGCNA modules to plot. All elements of modules2plot must be in the first element of net.
colors2plot	The colors for modules2plot. Must match the length of modules2plot.
kME.threshold	The kME threshold to retain a node
adjacency.threshold	The adjacency threshold to retain an edge.
adj.power	The power used to calculate the adjacency matrix
verbose	The position of the legend. Defaults to the top right.
node.size	If >0, plot the nodes with a given size.
frame.color	If node.size > 0, can specify the color for node outlines
node.color	If node.size > 0, can specify the color for nodes
edge.alpha	Numeric [0-1] specifying the transparency of the edges
returnNet	Should the network be returned? If FALSE, a list of the genes and original module colors that were input is returned.
...	additional arguments passed on WGCNA::adjacency

Details

More here soon.

Value

an igraph network

Examples

## Not run: 
library(WGCNA)
library(igraph)
data(kidney) #' from simseq
counts<-kidney$counts
counts<-counts[sample(1:nrow(counts),1000),]
info<-with(kidney,
           data.frame(id = paste(replic, treatment, sep = "_"),
                      rep=replic,
                      Treatment=ifelse(treatment == "Tumor","tumor","cntr"),
                      stringsAsFactors=F))
colnames(counts)<-info$id
stats <- pipeLIMMA(counts = counts,
                   info = info,
                   block = NULL,
                   formula = "~ Treatment")

datExpr.1=t(stats$voom$E)
pow=6
net.1 = blockwiseModules(datExpr.1, power = pow,
                         maxBlockSize = 10000, deepSplit = 2,
                         minModuleSize = 10,
                         saveTOMs = FALSE,
                         verbose = F)

graph<-wgcna2igraph(net = net.1, datExpr = datExpr.1,
                    modules2plot = c("blue","green","turquoise","brown"),
                    colors2plot = c("orange","darkred","cyan","cornflowerblue"),
                    kME.threshold = 0.5, adjacency.threshold = 0.1,
                    adj.power = pow, verbose = T,
                    node.size = 0, frame.color = NA, node.color = NA,
                    edge.alpha = .5, edge.width =1)
plot(graph)

## End(Not run)

jtlovell/RNAseqDE documentation built on May 10, 2019, 8:06 a.m.