Question: WGCNA network visualisation in RCyjs
0
gravatar for chrisclarkson100
2.9 years ago by
European Union
chrisclarkson10070 wrote:

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 • 1.2k views
ADD COMMENTlink modified 2.9 years ago by Jean-Karim Heriche18k • written 2.9 years ago by chrisclarkson10070

Cross-posted on bioconductor.org.

ADD REPLYlink written 2.9 years ago by Jean-Karim Heriche18k
1
gravatar for Jean-Karim Heriche
2.9 years ago by
EMBL Heidelberg, Germany
Jean-Karim Heriche18k wrote:

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

ADD COMMENTlink written 2.9 years ago by Jean-Karim Heriche18k
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