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#This is function to plot a dendrogram and display node groups in colored modules
PlotDendrogram <- function(Adj_directed, minModuleSize = 5, groupLabels = " ", dendroLabels = FALSE, hclustHang = 0.03, dendroAddGuide = FALSE, dendroGuideHang = 0.05, dendroMain = "Dendrogram with modules of nodes in colors", ...) {
#Adj_directed is a matrix from directed graph
#Start to find Module based on library(WGCNA)
#convert to a symmetric matrix because Adj_directed is not symmetric
Adj_symmetric_matrix <- Adj_directed
for (i in 1:nrow(Adj_symmetric_matrix))
{
for (j in 1:ncol(Adj_symmetric_matrix))
{
if(Adj_symmetric_matrix[i,j] == 1)
{
Adj_symmetric_matrix[j,i] <- 1
}
}
}
#Adj_symmetric_matrix is symmetric matrix after converting
TOM <- TOMsimilarity(Adj_symmetric_matrix); #Need Symmetric matrix
dissTOM <- 1-TOM
#Call the hierarchical clustering function from fastcluster
#This hclust that provides a much faster hierarchical clustering routine than the standard hclust function.
#geneTree = fastcluster::hclust(as.dist(dissTOM), method = "average");
geneTree <- hclust(as.dist(dissTOM), method = "average");
# Plot the resulting clustering tree (dendrogram)
#plot(geneTree, xlab="", sub="", main = "Gene clustering on TOM-based dissimilarity",
#labels = FALSE, hang = 0.04);
# Module identification using dynamic tree cut:
#The Dynamic Tree Cut may identify modules whose expression profiles are very similar.
dynamicMods <- cutreeDynamic(dendro = geneTree,
distM = dissTOM,
deepSplit = 2,
pamRespectsDendro = TRUE,
minClusterSize = minModuleSize);
Grouplist <- table(dynamicMods)
#print(Grouplist) #0=means unassigned genes
# Convert numeric lables into colors
dynamicColors <- labels2colors(dynamicMods)
Colorlist <- table(dynamicColors)
#print(Colorlist)
#sizeGrWindow(20,6);
PlotDendrogramObj <- plotDendroAndColors(dendro = geneTree,
colors = dynamicColors,
groupLabels = groupLabels,
dendroLabels = dendroLabels,
hang = hclustHang,
addGuide = dendroAddGuide,
guideHang = dendroGuideHang,
main = dendroMain, ...)
return(list(graph = PlotDendrogramObj,
dynamicColors = dynamicColors,
GroupMods = Grouplist,
GroupModsColors = Colorlist,
Adj_symmetric_matrix = Adj_symmetric_matrix))
}
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