STRING app Customizing network appearance

[Shraddha Pai]

Hi,

How do I change the network label font size for a STRING network generated in Cytoscape?

I am able to generate a network using a gene list, but thereafter I cannot use the node attribute "Label font size" to make the labels bigger.

Similarly, I cannot map the node colour to a discrete mapping ("if column value is TRUE, make node red, else make node grey").

I'm using stringApp v2.2.0 in Cytoscape 3.10.2 on an M1 Mac running Sequoia 15.2.

Thanks,

Shraddha

[Shraddha Pai]

Hello, nevermind - looks like I just needed to change the "Style" from "STRING" to "default", and then had control over the attributes. Leaving the solution here for posterity.

S

[Odinaka Chris Iwuozo]

Hi,

I installed Cytoscape 3.10.3 on Windows x64, but I can't launch or open the software on my laptop. Meanwhile, required Java 17 is already installed. I will appreciate guidance on how to navigate this.

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[Christopher Churas]

Hi,

Sorry to hear you are having problems. When you say windows x64, is it windows 10 or 11?

To help troubleshoot could you run the troubleshooting script found here:
https://cytoscape.org/troubleshooting.html

You might have to right click on the "Download for Windows" button and choose "save link as"

If using Edge browser, you will need to "keep" the download. I believe chrome just warns you, but does save it.

Once done navigate to your downloads folder and double click on the windows.bat
What is the output in the window (take a screenshot or copy the text)

Another thing to try. 

Navigate to C:\Program Files\Cytoscape_v3.10.3 folder and double click on cytoscape.bat (does cytoscape launch?)

While in the folder do you see an .install4j folder within?

chris

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[Odinaka Chris Iwuozo]

Hello,

Thank you for the prompt response.

Yes, my computer is Windows 11, I meant x64 bits.

I navigated to the folder in the C:\Program Files\Cytoscape_v3.10.3. 

I found the .install4j folder, but unfortunately, the Cytoscape does not launch after the double click.

I appreciate your guidance for the next steps. Thank you for your time.

Sincerely,

Odinaka

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[Christopher Churas]

Hi,

Sorry for the delayed reply. If you only installed java for Cytoscape, I suggest uninstalling both Cytoscape and Java and then try installing Cytoscape again.

Cytoscape should detect no Java is installed and offer to download a copy to be placed within Cytoscape. Be sure to allow that

download and hopefully Cytoscape will work when launched. 

If not please try running the trouble shooter script:
https://cytoscape.org/troubleshooting.html

and send back the output.

thanks,

chris

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[Odinaka Chris Iwuozo]

Hello Chris,

Thank you for your email.

The suggestion was helpful. I have been able to launch the Cytoscape 3.10.3!

I will navigating the Cytoscape for the first time. I will be ready to ask additional questions while navigating this platform for my Omics studies.

My sincere regards,

Odinaka

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