Cytoscape KEGG plots reverting to original layout after changing style or column

Question

[Adrian]

I'm trying to use cytoscape to better plot kegg pathways. I've obtained xml files from pathview and imported via "import network via file system".

Problem 1: Missing quite a lot of info especially arrows and certain symbols like small circle or rectangle. It also created many arrows that arent present from the pathview png output.

Problem2: Probably a cytoscape issue, but whenever I change the style even just the font size, all the nodes reverts back to original position after painstakingly moving them one by one.

Is there any workarounds for these problems?

Thanks in advance

Answer 1

[Scooter]

I have no idea about problem 1. My best guess is that there are glyphs in the png that aren't supported by Cytoscape, but I'm not a KEGG expert. As to Problem 2, my guess is that the positions are defined by Bypass values that are passed in the node table. To see if that's the case, go to the Style panel and select "More Properties...". Add the X Location and Y Location properties. Then, select all of the nodes and see if there is anything in the Bypass (Byp.) column for the X Location and Y Location properties. If there is, click on it and select "Remove Bypass". Then you should be able to move things around without having it reset.