<p>Happy to help. The Cytoscape team answers questions here weekly.</p>
<p>What you want to do is definitely doable. Coloring nodes is managed in the Style panel (on the left). You can set a default color (i.e., for all the nodes without phosphoproteomics data values) by clicking on the left-most box for the Fill Color property. Then you can click on the middle box to define a gradient color over the range of values in a particular column.</p>
<p>Nodes that have values will have a gradient color. Nodes without a value will be the default color.</p>
<p>Here are relevant sections of the manual and a tutorial:</p>
<ul>
<li><a href="https://manual.cytoscape.org/en/stable/Styles.html" rel="nofollow noreferrer">https://manual.cytoscape.org/en/stable/Styles.html</a></li>
<li><a href="https://cytoscape.org/cytoscape-tutorials/protocols/basic-data-visualization/#/" rel="nofollow noreferrer">https://cytoscape.org/cytoscape-tutorials/protocols/basic-data-visualization/#/</a></li>
</ul>

CC BY-SA 4.0
2024-10-10T17:40:23.980Z
2024-10-10T17:40:23.980Z
AlexanderPico
<p>I uploaded the network map of the protein of interest using String to cytoscape. Similarly, I was able to input protein and fold change data that were changing in phosphoproteomics into cytoscape. I was also able to do a simple merge of these two pieces of data. The problem I have is that I want to change the color of only those identified by phosphoproteomics in the STRING network, but I don't know how. Furthermore, I would like to create a gradation for the color depending on the amount of change. Please tell me how to do it. thank you.</p>

CC BY-SA 4.0
2024-10-06T12:10:30.367Z
Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking.
Community
CC BY-SA 4.0
2024-10-07T11:25:11.463Z
Please [edit] your question and show us the actual data. Not all, but a few represenative lines of the various data file you have loaded so we know what you are working on. Then, explain what information should be used to color (what? nodes? edges?).
terdon
<cytoscape>
How to overlay string data and phosphoproteomics data in cytoscape
# How to overlay string data and phosphoproteomics data in cytoscape

(Asked by: username_0 on 2024-10-06)

I uploaded the network map of the protein of interest using String to cytoscape. Similarly, I was able to input protein and fold change data that were changing in phosphoproteomics into cytoscape. I was also able to do a simple merge of these two pieces of data. The problem I have is that I want to change the color of only those identified by phosphoproteomics in the STRING network, but I don't know how. Furthermore, I would like to create a gradation for the color depending on the amount of change. Please tell me how to do it. thank you.

**Tags:** cytoscape
> **Comments:**
> **username_1**: Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking.  
> **username_2**: Please [edit] your question and show us the actual data. Not all, but a few represenative lines of the various data file you have loaded so we know what you are working on. Then, explain what information should be used to color (what? nodes? edges?).  

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## 1 answers

### Answer by username_3 on 2024-10-10. Score: 0

Happy to help. The Cytoscape team answers questions here weekly.

What you want to do is definitely doable. Coloring nodes is managed in the Style panel (on the left). You can set a default color (i.e., for all the nodes without phosphoproteomics data values) by clicking on the left-most box for the Fill Color property. Then you can click on the middle box to define a gradient color over the range of values in a particular column.

Nodes that have values will have a gradient color. Nodes without a value will be the default color.

Here are relevant sections of the manual and a tutorial:

* <https://manual.cytoscape.org/en/stable/Styles.html>
* <https://cytoscape.org/cytoscape-tutorials/protocols/basic-data-visualization/#/>


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