Question: How to annotate nodes in Cytoscape
gravatar for lagartija
2.2 years ago by
lagartija90 wrote:

Hi everyone,

Do you know cytoscape ? I have a network of 5900 nodes that I want to label them with the gene name (one column of my annotation table). Do you know how I can do that without having to do it manually ? I came accross this app that can be usefull AutoAnnotate but it doesn't work for me as it clusters the nodes before the annotation (and I just want the name inside the single nodes).

I also created filters to differentiate specific nodes. Do you know how to apply a style to a specific filter only ?

Thank you very much in advance, Sofia

software error • 2.3k views
ADD COMMENTlink modified 2.2 years ago • written 2.2 years ago by lagartija90

Please use ADD COMMENT/ADD REPLY when responding to existing posts to keep threads logically organized. This comment belonged under answer provided by @Jean-Karim.

SUBMIT ANSWER should only be used for new answers for original question.

ADD REPLYlink written 2.2 years ago by genomax87k

Thank you. That was what I was doing all this time. I tried again from scratch and it seems it works but I loose it when I change to organic layout. Actually I just understood that my problem is very stupid. When I zoom in A LOT I can see the label, otherwise I can not even if I change the size of the font. Not very practical... And not much I can do about it neither; Maybe the version 6.1 has a problem with that (because I did not notice that on the display with other versions).

ADD REPLYlink modified 2.2 years ago • written 2.2 years ago by lagartija90

Problem almost solved : the labels are not visible on the cytoscape session but when I save the image the labels are visible. I just have to take a look at the save images to edit my network correctly :)

ADD REPLYlink written 2.2 years ago by lagartija90
gravatar for Jean-Karim Heriche
2.2 years ago by
EMBL Heidelberg, Germany
Jean-Karim Heriche23k wrote:

Use the Style tab in the control panel and select the gene name column with passthrough mapping as node label property. See the styles docs.

ADD COMMENTlink written 2.2 years ago by Jean-Karim Heriche23k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 710 users visited in the last hour