WGCNA convenience function
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Entering edit mode
3 months ago
fluentin44 • 0

Hi,

I'm using the below code in a WGCNA worfkflow

# memory estimate w.r.t blocksize
bwnet <- blockwiseModules(norm.counts,
                          maxBlockSize = 14000, # Genes included in one block
                          TOMType = "signed",
                          power = soft_power,
                          mergeCutHeight = 0.25, # Threshold to merge modules Equates to 75% similarity - go and check
                          numericLabels = FALSE, # Sets module eigengene labels to be names of colours instead of numbers
                          randomSeed = 1234,
                          saveTOMs = TRUE,
                          saveTOMFileBase = "./",
                          verbose = 3)

and making the subsequent dendrogram.

# Plot the dendrogram and the module colors before and after merging underneath
plotDendroAndColors(bwnet$dendrograms[[1]], cbind(bwnet$unmergedColors, bwnet$colors),
                    c("unmerged", "merged"),
                    dendroLabels = FALSE,
                    addGuide = TRUE,
                    hang= 0.03,
                    guideHang = 0.05)

when I plot bwnet$unmergedColors, bwnet$colors as above, which I understood to be the unmerged and merged modules I get a dendrogram looking like the below which shows a reasonable merge

version1

However when using the labels2colors function as suggested in the WGCNA tutorial I get a far more dramatic change when plotting out?

mergedColors <- labels2colors(bwnet$colors)

# Plot the dendrogram and the module colors before and after merging underneath
plotDendroAndColors(bwnet$dendrograms[[1]], cbind(bwnet$unmergedColors, mergedColors[bwnet$blockGenes[[1]]]),
                    c("unmerged", "merged"),
                    dendroLabels = FALSE,
                    addGuide = TRUE,
                    hang= 0.03,
                    guideHang = 0.05)

version2

Would anyone be able to tell me:

  • Which are the merged modules I should be using?
  • What is the purpose of labels2colors if the blockwiseModules function I used specified numericLabels = FALSE?

Thanks,
Matt

WGCNA • 330 views
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1
Entering edit mode

I don't really understand what is going on here. It seems that

mergedColors <- labels2colors(bwnet$colors)

just changed the colors of the merged Modules -> eg gray to black or turquoise to midnightblue etc.

Which are the merged modules I should be using?

In terms of gene content they are the same. I would go with the first set of merged modules because the "grey" color is typically used for the unassigned genes.

What is the purpose of labels2colors if the blockwiseModules function I used specified numericLabels = FALSE?


update: After looking at the blockwiseModules function it seems that the numericLabels argument is bypassed by default when performing the merging module step.

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Entering edit mode

Apologies for neglecting - followed the manual method in the end and wored great.

Thanks, Matt

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