Description about the output

[harimchun]

Description about the output

[adugourd]

Hi Harim,

Thanks for your interest in our tool :)

P means "Perturbed", these are nodes that were given in the input paramater of the carnvial function.

M means "Measured", these are the nodes that were given as measurements parameter to the carnival function.

The best way to import the result in cytoscape is simply to export the weightedSIF and nodesAttributes table as CSV files (see code under)

SIF <- as.data.frame(carni_res$weightedSIF)
ATT <- as.data.frame(carni_res$nodesAttributes)

write_csv(SIF, file = "results/SIF.csv")
write_csv(ATT, file = "results/ATT.csv")

Then you can import those files as SIF network and Attributes in cytoscape (you have buttons for that in the toolbar of cytoscape.

You can then adjust the style to your liking :)

Cheers,

Aurelien

[harimchun]

Thank you for the reply, Aurelien!

It really helps a lot!

I also think using Cytoscape for the visualization is the best way.
Then how about using the "carnival_visNet" from the transcript tutorial? I think it utilizes visNetwork and is quite simple to visualize the network.

Thanks!

Best,
Harim

[adugourd]

Hi Harim,

It can be use with some tinkering of the code, but for simplicity, it's probably better to stick with cytoscape for now :)

Cheers,

Aurelien

[harimchun]

Thanks!

I'll try Cytoscape.