coloring my nodes in cytoscape network

[atira]

hi dear,
i have a big network comprising up and down regulated genes (differentially expressed genes). i want to color nodes in different color. up regulated genes:green and down regulated genes:red.

how can i do this?

anyone can help me?

[piet molenaar]

Hi,

This can be done, it is actually what Cytoscape is made for.

In this tutorial you can find out how: https://cytoscape.github.io/cytoscape-tutorials/protocols/modules/mapping-data/#/

It is part of the new and fully updated tutorials wiki: https://github.com/cytoscape/cytoscape-tutorials/wiki 

In short, you should use a visual style; open the style tab in the left panel, make sure the node tab is selected. Click on the Fill Color row and select the proper data column containing the expression values. Set the mapping type to continuous and select the color and gradient values to your liking.

Hope this helps,

Piet

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Piet Molenaar
piet...@gmail.com
Department of Oncogenomics, M1-131
Academic Medical Center
University of Amsterdam
Meibergdreef 9
1105 AZ Amsterdam
the Netherlands

tel (+31) 20-5666592
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[atira]

thanks for your guidance

i constructed ppi network in "string database" and visualized in cytoscape so i don't have expression values. in this case i have name, shared name and selected in the fill color of style panel. therefore all nodes become one-color.

please help me?

[piet molenaar]

Well, for this to be visualized the data has to be entered into Cytoscape. 

In what format is your expression data?

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[t.cher...@gmail.com]

On Tuesday, March 13, 2018 at 4:57:08 PM UTC+3:30, Piet wrote:
> Well, for this to be visualized the data has to be entered into Cytoscape. 
> In what format is your expression data?
>
>
>
>
> On Tue, Mar 13, 2018 at 2:15 PM, atira <t.cher...@gmail.com> wrote:
>
>
>
>
> thanks for your guidance
>
>
>
> i constructed  ppi network in "string database" and visualized in cytoscape so i don't have expression values. in this case i have name, shared name and selected  in the fill color of style panel. therefore all nodes become one-color.
>
>
>
> please help me?
>
>
>
> --
>
> 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/c169f655-a075-4403-8c6e-057af9c5b289%40googlegroups.com.
>
>
>
> For more options, visit https://groups.google.com/d/optout.
>
>
>
>
>
> --
>
> Piet Molenaar
> piet...@gmail.com
> Department of Oncogenomics, M1-131
> Academic Medical Center
> University of Amsterdam
> Meibergdreef 9
> 1105 AZ Amsterdam
> the Netherlands
>
> tel (+31) 20-5666592
> fax (+31) 20-6918626

i constructed my network in string database by entering interested proteins and visualized in cytoscape. string file is "txt".