[R] WGCNA: Combining block-wise dendrograms and modules into a single figure

[Derek55]

Hello fellow R users,

I am currently learning to use R, so please forgive me if there is an
obvious explanation for the following problem. My goal is to perform WGCNA
on a dataset of 19776 genes, so I opted to follow the block-wise network
construction (Section 2c) in the WGCNA R Tutorial by Peter Langfelder and
Steve Horvath.

I ended up with 10 blocks and am able to plot the dendrograms and module
colors for each block, but I am having trouble grouping all of the blocks
together for a single dendrogram/module color figure. On page 4 of section
2c in the WGCNA tutorial, the single-block network construction workspace is
loaded and it contains a variable called 'geneTree'. geneTree references
block 1 of the single-block network construction, which encompasses the
entire dendrogram.

geneTree = net$dendrograms[[1]]

The problem here is that I cannot perform single-block construction because
I do not have enough RAM, so I do not know how to reproduce the complete
dendrogram using the blocks that I am currently working with. If I had
simply reused the same definition for geneTree using the block-wise network,
it would simply print block 1 out of 10 blocks (I have already tried this).

Session Information:

R version 2.15.1 (2012-06-22)
Platform: i386-pc-mingw32/i386 (32-bit)

locale:
[1] LC_COLLATE=English_United States.1252 
[2] LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] splines   stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
 [1] WGCNA_1.23-1        MASS_7.3-18         reshape_0.8.4      
 [4] plyr_1.7.1          cluster_1.14.2      Hmisc_3.9-3        
 [7] survival_2.36-14    flashClust_1.01-2   dynamicTreeCut_1.21
[10] impute_1.32.0      

loaded via a namespace (and not attached):
[1] grid_2.15.1    lattice_0.20-6



I have tried several methods for compiling the separate dendrograms together
for the complete figure:

Input:

plotDendroAndColors(bwnet$dendrograms[[1:10]],
bwModuleColors[bwnet$blockGenes[[1:10]]],
                  "Module colors",
                  dendroLabels = FALSE, hang = 0.03,
                  addGuide = TRUE, guideHang = 0.05)

# Above, 'bwnew$dendrograms[[x]]' is equivalent to the parameter specified
by 'geneTree', but must be changed each time to plot blocks 1-10
# In addition, bwModuleColors[bwnet$blockGenes[[x]]] should be changed with
the parameters for the geneTree equivalent

 Output: 

"Error in bwnet$blockGenes[[1:10]] : recursive indexing failed at level 2"

Input: 

Same as above, changing bwnet$dendrograms[[1:10]] to bwnet$dendrograms[1:10]
and bwModuleColors[bwnet$blockGenes[[1:10]]] to
bwModuleColors[bwnet$blockGenes[1:10]]

Output:

"Error in bwModuleColors[bwnet$blockGenes[1:10]] :
    invalid subscript type 'list' "

Input:

Same as above, but changed bwModuleColors[bwnet$blockGenes[1:10]] back to
bwModuleColors[bwnet$blockGenes[[1:10]]]

Output:

"Error in bwnet$blockGenes[[1:10]] : recursive indexing failed at level 2"

Any of these examples could be replicated straight from the tutorial using
the mouse data and trying to combine block 1 and block 2 without loading and
referencing the auto-network construction workspace.

Thank you very much for your time and input,

~Derek



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