Question: interactive networks from WGCNA clusters
1
gravatar for christopher.clarskon15
3.2 years ago by
christopher.clarskon1520 wrote:

 

I am trying to get an interactive network to deploy from a pipeline of WGCNA steps. I would like to be able to upload a file that can be read into a data frame and processed to make a network. Below is the code that I have used to identify modules in the gene-network:

p1<-adjacency(E.rna_small,type=input$adj)
.....
p1<-p1[keepSamples, ]
ADJ1=abs(p1)^6
dissADJ1<-1-ADJ1
hierADJ=hclust(as.dist(dissADJ1), method="average" )

 

As you can see, the above code is taken from WGCNA's sample tutorials. I have managed to plot the modules:

enter image description here

The separation is not very good because I am simply uploading a sample file that gets processed to a 20X20 adjacency matrix. 

My problem is that I can not get these clusters to manifest in the interactive network that I am deploying, done as follows: 

library(igraph)

library(rcytoscapejs)

edge<-as.data.frame(get.edgelist(simplify(graph_from_adjacency_matrix(p1, weighted=T))))

colnames(edge)<-c("source", "target")

nodes<-cbind(id=colnames(p1), name=rownames(p1))
nodes<-as.data.frame(nodes)
g<-createCytoscapeJsNetwork(nodeData = nodes, edgeData = edge)

rcytoscapejs(g$nodes, g$edges)

The network has no structure though i.e. no modules are present in this network...

enter image description here

Hence what I am wondering is how can I get the clustered modules to show in the deployed network, something like this:

enter image description here

My attempt at making the modules manifest in the graph thus far are as follows:

Somehow integrating the hclust output of WGCNA into the rcytoscape data via the command "setLayoutProperties", which takes the arguments obj, layout.name, properties.list. Can I somehow put the information of hclust (class(hclust(input)) <- "hclust") into the "properties.list" argument...?

My other strategy follows the instructions of the WGCNA tutorial:

TOM = TOMsimilarityFromExpr(p1, power = 6);
modules = c("brown", "red"); #don't necessarily want to pre-assign modules rather than discovering them...
probes = names(p1)
inModule = is.finite(match(moduleColors, modules));
modProbes = probes[inModule];
modGenes = annot[1:20, 1:20]$gene_symbol[match(modProbes, annot[1:20, 1:20]$substanceBXH)];

modTOM = TOM[inModule, inModule];
dimnames(modTOM) = list(modProbes, modProbes)
# Export the network into edge and node list files Cytoscape can read
cyt = exportNetworkToCytoscape(modTOM,
                               edgeFile = paste("CytoscapeInput-edges-", paste(modules, collapse="-"), ".txt", sep=""),
                               nodeFile = paste("CytoscapeInput-nodes-", paste(modules, collapse="-"), ".txt", sep=""),
                               weighted = TRUE,
                               threshold = 0.02,
                               nodeNames = modProbes,
                               altNodeNames = modGenes,
                               nodeAttr = moduleColors[inModule]);

 

However I get the following error when trying to export the network:

Error in exportNetworkToCytoscape(modTOM, edgeFile = paste("CytoscapeInput-edges-",  : 
  Cannot determine node names: nodeNames is NULL and adjMat has no dimnames.

Overall I just want to know how to get the modules given by the dendogram above to display in the interactive graph... Preferably I would like to be able to do this without having to upload a separate annotation file and pre-assign module colours as is done in the final bit of code above- modules = c("brown", "red").

What would be most convenient is if I could is if I could specify the layout within the rcytoscapejs command:

net = blockwiseModules(p1, maxBlockSize = 2000,
                         power = 6, TOMType = "unsigned", minModuleSize = 2,
                         reassignThreshold = 0, mergeCutHeight = 0.25,
                         numericLabels = TRUE,
                         verbose = 3)

rcytoscape(g$nodes, g$edges, layout=net$blocks)

rcytoscape wgcna • 1.4k views
ADD COMMENTlink modified 3.2 years ago by branislav misovic120 • written 3.2 years ago by christopher.clarskon1520

you mean these tutorials ?
https://labs.genetics.ucla.edu/horvath/CoexpressionNetwork/Rpackages/WGCNA/Tutorials/index.html

ADD REPLYlink written 3.2 years ago by branislav misovic120
Answer: interactive networks from WGCNA clusters
2
gravatar for Paul Shannon
3.2 years ago by
Paul Shannon370
Paul Shannon370 wrote:

Hi Chris,

Have you tried using one of the cytoscape.js native layouts?  For instance:

 

 layout(rcy, "cose")

Where rcy is an RCyjsClass object

 

There are a handful of cyjs layout strategies.

   layoutStrategies(rcy)

will show you the full list.  cose is a "Compound Spring Embedder" and
may give you a good start on the layout you want.  Because automated
layouts almost always come up somewhat short of elegance, you can fine
tune the layout by hand, then call

saveLayout(rcy, "yourFileName.RData")

for later reuse.

Where is the function "exportNetworkToCytoscape" defined?  It apparently does not like the arguments you supplied, but without knowing what those are it is hard to guess at the cause of the error you see.

 - Paul

 

ADD COMMENTlink modified 3.2 years ago • written 3.2 years ago by Paul Shannon370
Answer: interactive networks from WGCNA clusters
0
gravatar for christopher.clarskon15
3.2 years ago by
christopher.clarskon1520 wrote:

The following code allowed me to colour the nodes according to their blockGene... 

net = blockwiseModules(E.rna_small, maxBlockSize = 2000,
                         power = 6, TOMType = "unsigned", minModuleSize = 2,
                         reassignThreshold = 0, mergeCutHeight = 0.25,
                         numericLabels = TRUE,
                         verbose = 3)

B<-createCytoscapeJsNetwork(nodeData = nodes, edgeData = edge, nodeColor = net$blockGenes)
rcytoscapejs(B$nodes, B$edges)

But this is because the net$blockGenes output is simply 1-20 the nodes are all coloured black....

when I try nodeColor = net$colors I get an error:

Error in `$<-.data.frame`(`*tmp*`, "color", value = list("turquoise",  : 
  replacement has 400 rows, data has 20

Even though I've checked and there are 20 It is the same for all of the other net$ arguments...... unique(net$colors) returns that there are 60 rows....

Having looked at net$MEs has 20 rows and 3 columns explaining that there are 60 rows as above said.....

B<-createCytoscapeJsNetwork(nodeData = nodes, edgeData = edge, nodeColor = net$MEs[1])
rcytoscapejs(B$nodes, B$edges)

This works but it colors the nodes improperly......

ADD COMMENTlink modified 3.2 years ago • written 3.2 years ago by christopher.clarskon1520
Answer: interactive networks from WGCNA clusters
0
gravatar for branislav misovic
3.2 years ago by
Netherlands/Amsterdam
branislav misovic120 wrote:

hi I would propose you   to also try   BioC package  RedeR:
https://www.bioconductor.org/packages/release/bioc/vignettes/RedeR/inst/doc/RedeR.pdf

I used it for nesting and clustering .

not to forget ,   big  Thank you to   Paul for great work   on   many   packages

Best,
Branko
p.s.
our security policies at hospital do not allow us to go to http://i.stack.imgur.com

ADD COMMENTlink written 3.2 years ago by branislav misovic120
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