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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