gene regulatory network visualization

Question

[zizigolu]

hi

I have a small expression datasets like below

head(data[,1:4])

       treatment1 treatment2 control1 control2

1 244906_at 7.694273 6.390339 11.420760

2 244950_at 7.972370 6.144543 10.554545

I inferred a gene regulatory network like so

library(minet)

mim <- build.mim(t(data),estimator="spearman")

net <- aracne(mim)

library(igraph)

I converted network to an graph

g <- graph.adjacency(net,mode="directed",weighted=T)

library(Rgraphviz)

library(RCytoscape)

g.cyto <- igraph.to.graphNEL(g)

g.cyto <- initNodeAttribute(g.cyto, attribute.name='weight', attribute.type='numeric', default.value=0.0) cw = CytoscapeWindow ("met_cluster_net", graph=g.cyto)

but always error

Cytoscape window named 'met_cluster_net' does not exist yet Error! "weight" edge attribute not initialized. You should call: initEdgeAttribute (graph, attribute.name, attribute.type, default.value) where attribute type is one of "char", "integer", or "numeric". example: g <- initEdgeAttribute (g, "edgeType", "char", "molecule") or: g <- initEdgeAttribute (g, "pValue", "numeric", 1.0) 1 uninitialized edge attribute/s

may some on give me some guidelines

thank you

[Jean-Karim Heriche]

I am not familiar with RCytoscape but the error message is telling you that you need to initialize the edges. It looks like you're calling Cytoscape before doing so. Check the docs and example here.

[zizigolu]

sorry

if this is my original data

treatment1 treatment2 control1 control2 1 244906_at 7.694273 6.390339 11.420760

2 244950_at 7.972370 6.144543 10.554545 after converting to a graph , how I can add node attributes to graph??