Question: gene regulatory network visualization
0
gravatar for F
3.2 years ago by
F3.4k
Iran
F3.4k wrote:

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

R gene • 1.1k views
ADD COMMENTlink modified 3.2 years ago • written 3.2 years ago by F3.4k
1

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.

ADD REPLYlink written 3.2 years ago by Jean-Karim Heriche20k

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??

ADD REPLYlink written 3.2 years ago by F3.4k
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