- edited description
Issue with variable's label when exporting network
Hello, its Arno Germond again,
I am using the following line of script to draw the network of genes:
net.result <- network(PLSMODEL, cex.node.name = 1, comp = 1:2, cutoff = 0.7, col.names = TRUE, row.names = axis, lty.edge = "solid", lwd.edge = 1, show.edge.labels = FALSE)
I noticed that in the net.result$gR object, the names of the variables (X and Y) were not taken into account, (there are replaced by a number), although that when drawing the network (on plot), the name appeared properly on the network figure (both X and Y when I use the above line of code).
The consequence of this "unlabelled" gR object, is that, when I export the network model into Cytoscape 3 for example, it will result in a network without labels. I could not find a way of "relabelling" the network with the white.graph function. Please can you show me a way of saving the variable names in the gR object?
To export the network to Cytoscape, I used: write.graph(net.result$gR, file = "corr_network_0.7.graphml", format = "graphml") I also noticed the "gml" format returns an error (as mentionned by Guivo) and cannot be opened in Cytoscape. The returned message is as follow: "There were 50 or more warnings (use warnings() to see the first 50)"
Thank you very much for your support, Best regards, Arno
Comments (5)
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reporter -
reporter - edited description
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repo owner -
assigned issue to
Issue also reported by Carine Genet (email 18th Sept) with data.
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assigned issue to
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Hi Germond,
Could you please try with the latest version 6.3.0 and tell us if the bug is still there?
Thanks!
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repo owner - changed status to resolved
I believe this has been resolved (talking to another user)
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