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I am trying to use Gephi to visualize differences between samples in the pathways between a fixed set of nodes. At the moment I'm doing this by dragging nodes into their desired positions and then coloring them while in "Overview". It would be better if I could specify node id's, positions and colors in the data file and thereby standardize the graphs for the different samples and be able to skip the manual adjustments. The nodes should always occupy the same positions in the graph and have the same colors and id's but the edges are different from one sample to the next. I'd be grateful if someone could post a small sample of a text data file readable by Gephi in which node position and color are specified. Thanks

There is a plug-in for the Data Library that will help you.

You can find it here:

https://marketplace.gephi.org/plugin/recast-column/

Once you install it, if you go to the "More Actions" menu button, you'll see a couple of options in the "Group 3" category called "Recast column," "Get standart," and "Set standart."

I've found this plug-in to be enormously valuable because it allows you use Gephi tools to assign colors, and 3-space coordinates in a layout, and then capture those using the "Get standart" function. Or, you can generate your own color values or 3-space coordinate values using your own tools or algorithms and then, using "Set standart," you can make Gephi recognize them.

This is a wonderful plugin (thanks, Taras Klaskovsky!), and I hope you find it useful, too.

Thanks very much for the useful suggestion Francis_Flavin. In the meantime I have started to rewrite my data extraction program so that it casts the data to be input to Gephi in GDF format (https://gephi.org/users/supported-graph ... df-format/). This seems to do the trick.