WGCNA | plotDendroAndColors ERROR
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Priya • 0
@9b616aec
Last seen 17 days ago
India

Hi all,

I'm currently running a WGCNA analysis. I started with "step-by-step network construction and module detection" provided by Richard Chen click here to see the git hub link. The following steps I've done.

#first calculated soft power
power = c(c(1:10), seq(from = 12,  to = 50, by = 2))

sft_test = pickSoftThreshold(norm_counts, powerVector = power, networkType = "signed", verbose = 5)

#calculated the adjacencies
softPower = 16
adjacency = adjacency(norm_counts, power = softPower)

TOM = TOMsimilarity(adjacency);
dissTOM = 1-TOM

#Clustering using TOM: produces dendrogram of genes
geneTree = hclust(as.dist(dissTOM), method = "average");

#module identification using dynamic tree cut
dynamicMods = cutreeDynamic(dendro = geneTree, distM = dissTOM, deepSplit = 2, pamRespectsDendro = FALSE, minClusterSize =30);
table(dynamicMods)

#convert numeric labels to colors
dynamicColors = labels2colors(dynamicMods)
table(dynamicColors)

#plot the dendrogram and colors underneath
pdf(file = "plots/gene_dendrogram_with_module_colors", width = 12, height = 9);
plotDendroAndColors(geneTree, dynamicColors, "Dynamic Tree Cut",dendroLabels = FALSE, hang = 0.03, addGuide = TRUE, guideHang = 0.05, main = "Gene dendrogram and module colors") 

When I'm plotting this dendrogram, following error has been encountered:

Error in rect(trafo1$x, trafo1$y, trafo2$x, trafo2$y, col = as.character(C[,  : 
  invalid color name 'dodgerblue3.1'

Can anyone suggest something to deal with this error.

Thank you!

plotDendroAndColor WGCNA • 119 views
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