Issue with variable's label when exporting network

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Issue #98 resolved
Germond created an issue

Hello, its Arno Germond again,

I am using the following line of script to draw the network of genes:

net.result <- network(PLSMODEL, = 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)

  1. Florian Rohart

    Hi Germond,

    Could you please try with the latest version 6.3.0 and tell us if the bug is still there?


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