Hi,
I'm looking for a way to display expression levels over time in Cytoscape (latest version). We were previously able to use DynamicXpr to do this. I have the signal network as well as expression levels output from a model over time and want to create a video in which the nodes change color corresponding to the expression level over time. Can anybody help?
The DynNetwork plugin for Cytoscape 3.x has an option for playing and recording. However, I never got it to work so in the end, I always export each time point as a png image, each image being named sequentially e.g. T01.png, T02.png,... then I used ffmpeg (or avconv on Ubuntu 14.x) to assemble them into a video, e.g.:
ffmpeg -framerate 1/2 -i T%02d.png video.mp4
See the ffmpeg docs here.
In case you wanted to also add a soundtrack (probably not recommended as it will be distracting but for fun):
ffmpeg -i video.mp4 -i star-wars-theme-song.mp3 -map 0:0 -map 1:0 -c:v copy -c:a copy output.mp4
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