node shape

[Mohammadian]

Hi there!

I have a tabular list of genes and transcription factors like:

TF Gene
HNF4A FABP1
HNF4A ANPEP
HNF4A APOA1
HNF4A APOC3
ZC3H11A MTTP
NFIC MTTP
EZH2 CHP2
AR APOA4
AR SLC26A3
TP63 RBP2

How can visualize TFs as circles and genes as rectangles? thanks. I
tried creating two new columns for gene and TF attributes but was
unsuccessful.

[Alex Pico]

Hi Mohammadian,

The tabular list is great for importing networks. But also need to import table data to serve as attributes for your nodes and interactions. A file like this for example:

Symbol Type

HNF4A TF

NFIC TF

FABP1 Gene

ANPEP Gene

… …

After creating your network (like you described below), then import this file as a table, matching the “Symbol” column with the “name” column of the network. This will add “Type” attributes to each of your nodes. You can then use the Style panel to map that “Type” information to any visual property you like, e.g., Node Shape (discrete mapping).

Give it a try and let us know if you get stuck.

 - Alex

--
You received this message because you are subscribed to the Google Groups "cytoscape-helpdesk" group.
To unsubscribe from this group and stop receiving emails from it, send an email to cytoscape-helpd...@googlegroups.com.
To post to this group, send email to cytoscape...@googlegroups.com.
Visit this group at https://groups.google.com/group/cytoscape-helpdesk.
To view this discussion on the web visit https://groups.google.com/d/msgid/cytoscape-helpdesk/CALqdc3f8LOUBaFZ__t2h_%3Du8MJebcM5_TDzU1k3mKGqJegQjkg%40mail.gmail.com.
For more options, visit https://groups.google.com/d/optout.

[Mohammadian]

Thank you Alex. It did work.

> https://groups.google.com/d/msgid/cytoscape-helpdesk/02192AA7-B678-4B71-9942-168D79F3ED20%40gladstone.ucsf.edu.