Create network from make_bipartite_network output in Cytoscape 3.5

[Yang]

Hi,

I am trying to create a network from the outputs of make_bipartite_network to Cytoscape 3.5. However, all the tutorial online that I can find seem outdated. Please help!

Thanks a lot!

Best,

Yang

[zhiying Guo]

Hello Yang,

Did you try this tutorial ? Maybe it helps.

Zhiying Guo

[Yang]

Hi, Zhiying,

Thanks for help!

Yes, I tried. But I don't have the same edge and node tables. I tried to create a network by importing "EdgeTable.txt" file with "Sample" as source and "OTU" as target. However, I cannot find "Import -> Attribute". I tried "Import -> Table" but not sure which text file I should use among "NodeAttrTable", "OTUNodeTable" and "SampleNodeTable". 

Thanks,

Yang

[zhiying Guo]

Hello Yang,

The help file of make_bipartite_network.py says that 

The output of this script is four files:

EdgeTable - table with connections between samples and observations.

OTUNodeTable - table with observations and their associated metadata.

SampleNodeTable - table with samples and their associated metadata.

NodeAttrTable - table with the node attributes specified by the user with the given options.

You should use EdgeTable as the input of Cytoscape, just follow the steps here 

Best,

Zhiying

[Yang]

Thanks a lot for help, Zhiying! I will try it!

My another question is Cytoscape 3.5 is different from the description in the "Making Cytoscape Networks" webpage, which I guess is a previous version of Cytoscape. Do you happen to know where VizMapper is in the current Cytoscape?

Thanks again!

Best,

Yang

[Jai Ram Rideout]

Hi Yang,

You might have better luck asking the Cytoscape community, since this is a question specific to that tool (Cytoscape isn't developed by the QIIME team). If anyone else is familiar with Cytoscape, please jump in!

Best,

Jai