Description Usage Arguments Details Value Examples
wgcna2igraph
Function to cull and plot WGCNA networks. Requires
igraph and WGCNA to be installed.
1 2 3 4 5 |
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 |
More here soon.
an igraph network
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 | ## 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)
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