Help with visualisation of two sets of data

[barl...@gmail.com]

Dear All,

I am relatively new to Cytoscape and I am having silly trouble in visualizing the data in Cytoscape.

Basically, I have two sets of enrichment result, one is 16 hour while another is 24 hour.
I successfully inserted the results of two points into Cytoscape using enrichment apps and it gave a nice network.

Now the problem is I do not know how to colour the node with p-value for both time points as I only can able to select one set point in the fill colour box at a time. My question is how to do for both time points?

Maybe It might be good if I can get an example of Cytoscape file that has two points so that I can follow roughly.


Thank you very much for your help and time,
Regards,
Krishna

[Alex Pico]

It depends on what you want to show. For example, do you want highlight those nodes that are significant at both time points or either time point? Is it important to you which of the two time points it’s significant?  Once you decide those things, then you need to prepare a column with that information. In a spreadsheet application, for example, you can “merge” information from two columns into a new column that describes the significance you care to highlight. Then map that single column to one or more visual style properties (like node border color and thickness).

That’s how I do it anyways :). There are many ways and no real convention or standard. In the end, it depends on what you want to communicate through your data visualization.

 - Alex

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[radhekrsna]

Hi Alex, 

Thanks for your reply. I want to show the p-value for each node at two different points something like below.

https://www.biorxiv.org/content/biorxiv/early/2017/12/12/232835.full.pdf.

 

Back to data, I do have the p-values on separate columns.  

I have watched many videos and tutorials, but I failed to solve this issue.

Thank you again

Regards

Krisna

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[radhekrsna]

I have attached the example of my problem to show it precisely. It should not be difficult as I am describing.

Thank you.

Krishna

On Sat, 29 Dec 2018 at 07:18, Alex Pico <alex...@gladstone.ucsf.edu> wrote:

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[Alex Pico]

Sure. That’s using two visual properties: Node Fill Color and Node Border Color. Assign 16h to onel and 24h to the other. Done!

 - Alex

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<16_24 hour.sif><16_24 hour.cys>

[radhekrsna]

OH, I didn't think about that. Thank you.

Regards

Krishna

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