Importing Network From Wgcna Into Cytoscape
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10.7 years ago
pixie@bioinfo ★ 1.5k

I have performed wgcna analysis and have obtained 2 files for importing the network into cytoscape, one edge file and another node (attribute) file. The edge file has the following columns:

fromNode toNode weight direction fromAltName toAltName

Os.9416.1.S1at Os.11330.1.S2at 0.1920219249 undirected Os02g33110.1 Os03g28260.1

I have selected the source and target for the first two columns and interaction from the 4th column. How can I use the weight column so that it reflects in the network in the form of edge width or the edge length ?

cytoscape network • 15k views
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10.6 years ago
Hayssam ▴ 280

I assume that you have no header in your network file indicating the names of the column and that you are using Cytoscape 2. When you import your network (File -> Import network as a table), right click on the third column header, give it an appropriate attribute name (e.g. "Weight"), then left click on the column (it should turn blue) to indicate that you want to import this attribute.

Once the network is built, select an edge, go to the data panel (Menu: View -> Show data panel if not visible), click on the "Edge attribute browser", click on the button with two checkboxes and two tickmarks (its tooltip indicate "Select all Attributes") Check that the weight column is there

Then go to the control panel (Left panel of cytoscape window), go to VizMapper, in the visual mapping browser, double click on the row "Edge line width". This should create an "Edge line width" entry under the "Edge visual mapping" table. In this entry, select "Weight" as the value; then "Continuous Mapper" as the Mapping type. Double click on the "Graphical View" of this mapping to fine tune how weight values are mapped to edge width.

You can have a look at these two screenshots detailing the setup:

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3.1 years ago

On Cytoscape 3.8.0, you can import WGCNA network by File -> Import -> Network from File and selecting the module edge file. On the import dialogue box, you will typically select the fromNode column as the Source Node and the toNode column as the Target Node. The weight column should be left as an Edge Attribute. The direction column should be changed to interaction type. fromAltName is a Source Node Attribute while the toAltName is a Target Node Attribute.

Entering edit mode

Dear Solo,

I have come across your responses and it was really helpful. I am using cytoscape to create a network from WGCNA module. You have explained very well on how to import the module edge file and it works with my file.

However, I am wondering how about the node file because the function exportNetworkToCytoscape generate edge file and node file. How could I use the node file with the edge file to create a network? Hope you could help and thank for your kind response here.

Kind Regards,


Entering edit mode

file->import->Table from File to import node file


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