WGCNA network visualisation in RCyjs
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5.2 years ago

I have used the Pearson correlation method to infer a network of interacting genes from microarray data. And ultimately, I would like to study this network with 'WGCNA'. However as useful as some of the commands in WGCNA seem, I can't find anywhere in the tutorials a command that actually allows me to visualise the networks.... So I instead used the package 'network' to plot and visualise this network.....

Subsequently I'd like to use 'RCyjs' to visualise the networks via javascript and ultimately create a website. Does anyone know if it is possible to jointly use shiny and RCyjs to make a pipeline that can accept microarray data and via these packages, produce a network?? Or should I try to use Django (if that's possible)?

p1<-cor(t(E.rna[1:20,1:20]),use="p") #pearson correlation

plot(as.network.matrix(p1)) #network package

RCyjs(portRange=9047:9057, quiet=TRUE, graph=as.network.matrix(p1));

RCyjs

Error in validObject(.Object) : invalid class “RCyjsClass” object: invalid object for slot "graph" in class "RCyjsClass": got class "network", should be or extend class "graph"

RCyjs does not seem to accept networks and instead only takes 'graphs'.... how can I rectify this? If possible could anyone recommend alternate packages?

RCyjs network WGCNA • 2.2k views
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Cross-posted on bioconductor.org.

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5.2 years ago

You could try the intergraph package. It converts graphs between network and igraph. The igraph graph class may be compatible with RCyjs.

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