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+s789695n4646661...@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 > > > > > > > > -- > > View this message in context: > http://r.789695.n4.nabble.com/WGCNA-Combining-block-wise-dendrograms-and-modules-into-a-single-figure-tp4646627.html > > Sent from the R help mailing list archive at Nabble.com. > > > > ______________________________________________ > > [hidden email] > > <http://user/SendEmail.jtp?type=node&node=4646661&i=1>mailing list > > https://stat.ethz.ch/mailman/listinfo/r-help > > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > > and provide commented, minimal, self-contained, reproducible code. > > ______________________________________________ > [hidden email] <http://user/SendEmail.jtp?type=node&node=4646661&i=2>mailing > list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > > > ------------------------------ > If you reply to this email, your message will be added to the discussion > below: > > http://r.789695.n4.nabble.com/WGCNA-Combining-block-wise-dendrograms-and-modules-into-a-single-figure-tp4646627p4646661.html > To unsubscribe from WGCNA: Combining block-wise dendrograms and modules > into a single figure, click > here<http://r.789695.n4.nabble.com/template/NamlServlet.jtp?macro=unsubscribe_by_code&node=4646627&code=ZGVyZWtncGVyZXpAdXRleGFzLmVkdXw0NjQ2NjI3fC05Mjg4MzQyNTQ=> > . > NAML<http://r.789695.n4.nabble.com/template/NamlServlet.jtp?macro=macro_viewer&id=instant_html%21nabble%3Aemail.naml&base=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespace&breadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml> > -- View this message in context: http://r.789695.n4.nabble.com/WGCNA-Combining-block-wise-dendrograms-and-modules-into-a-single-figure-tp4646627p4646671.html Sent from the R help mailing list archive at Nabble.com. 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