Cytoscape _v3.5.1 software

Question

[gokusri18]

hello greetings to all there,

I would like to ask the community here do anyone can explain and provide sample on how to upload table into cytoscape software and how to obtain outcome of dynamic graphical representations of transcription factors.I cannot find any simple tutorial and pls do help me for my research.

Answer 1

[Jean-Karim Heriche]

In Cytoscape 3.x, you import a table using the menu: File > Import > Table > File... For dynamic graphs, you have the DynNetwork app. By outcome of dynamical graphical representation, I assume you mean some sort of animation/movie of the graph evolution. I never succeeded in doing this with Cytoscape. The DynNetwork record function never worked for me and I ended up saving each time point as an image and using external software (e.g. ffmpeg) to combine the images into a movie.
Anyway, for dynamic networks I would recommend using R instead. The main reason is that Cytoscape is not very well suited for analyzing them. In R, you can represent your dynamic graph as a third order tensor (i.e. a 3-dimensional array) to which you can apply a range of analysis methods like for example tensor factorizations for clustering. You can also visualize dynamic graphs with R, see this tutorial for example. However, while movies of dynamic networks might look cool, they're often bad visualizations because even for small networks it is hard to get information out of them. There are often alternative representations that convey the relevant information better.

[gokusri18]

thank you very much for the response and explanation