Hi Peter,

Thank you for your time and input on this matter. I will take your advice
and reconstruct the blocks using a different maximum cutoff and plot the
figures next to one another. I also wanted to thank you for creating the
WGCNA package and including the section on exporting to other visualization
software, as I am currently using Cytoscape to make figures of the gene
networks.

All my best,
~Derek

On Thu, Oct 18, 2012 at 12:19 PM, plangfelder [via R] <
ml-node+s789695n4646661h66@n4.nabble.com> wrote:

> Hi Derek,
>
> the simple answer is that the block-specific dendrograms cannot be
> meaningfully combined into a single dendrogram. You have to plot them
> separately. You can create a multi-panel figure that shows all block
> dendrograms in one big figure, although with 10 blocks I would not
> necessarily attempt it.
>
> One comment that does not quite relate to your question but may still
> be relevant is that you seem to have too many blocks. Unless you have
> a really old computer with 1GB RAM or less, the block size you used is
> likely too small. (The tutorial uses a small block size to illustrate
> the approach.)  If you have 4GB RAM, try maxBlockSize = 8000. If you
> have 8GB, you can try maxBlockSize about 12000.  You will get fewer
> blocks and most likely a better clustering/modules.
>
> Best,
>
> Peter
>
> On Thu, Oct 18, 2012 at 7:33 AM, Derek55 <[hidden email]<http://user/SendEmail.jtp?type=node&node=4646661&i=0>>
> wrote:
>
> > 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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> >
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