Cytoscape visualisation issue

Question

[sarah.laverty20]

Hi all,

I am using cytoscape to create a protein interaction network following one of their tutorials.

I have followed everything apart from being unable to select 'query term' for node table columns section when uploading my table with fold change and p-value information. My only options are 'select interaction' or 'select protein'. I chose select protein because a warning came up when I clicked on interaction.

I am able to edit the network in the way I want to apart from changing the node fill colour to continuous mapping for fold change or p-value. There is no colour change when I select these options. I am wondering if anyone has had similar problems and if they would be able to help.

Thanks in advance.

Answer 1

[scooter]

Hi Sarah,

You shouldn't see "interaction" in your list. This probably means that Cytoscape thinks you are importing an edge table rather than a node table. There is an issue in 3.9.1 where the edge table pops up by default when you open a network (in previous versions it used to be the node table). So, go back and before you do your import table, make sure the node table is selected in Cytoscape. Once that's done, you can do the import and the import dialog should say that it's importing a node table. The query term should now be one of your options. Let us know if that isn't the case!

-- scooter

[sarah.laverty20]

Hi there, That worked thanks so much!

I have a secondary question:

I have now made an interaction network and I am happy with the outcome apart from the fact there is a lot of overlapping of the nodes and therefore you can't read some of the names of the genes stated (see image). Is there a way to format it so that this doesn't happen?