How to make each node clear?

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sandra yin

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Jun 16, 2019, 2:30:39 PM6/16/19
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Hi, 

Thanks in advance for your help. 
After I put in my network dataset, it generated this interaction map. 
Two questions: 
1. Do the length of the line or size of the node correspond to any quantitative information I put in? I did have p-value and fold change in my table. 
2. Is there a convenient way to make the entire interaction map more spread out, so that the nodes don't overlap?

Thank you very much. 

Screen Shot 2019-06-16 at 11.25.36 AM.png

Alex Pico

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Jun 16, 2019, 2:52:47 PM6/16/19
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Hi Sandra,

You’ve hit upon two of the most common uses for Cytoscape: data mapping (i.e., using data values to control visual properties) and layout. There are a ton of features related to these types of operations. I recommend starting with one of our tutorials:

Browse the other tutorials there as well and check out some of the videos at:

There is a video for example on layouts and how to “spread out” nodes using Node Layout Tools: 

To address your specific questions:
 1A. Some layouts support using attribute values. See "Edge-weighted …” layouts in the Layout menu
 1B. P-value on fold changes sounds like a node-based measure. You’ll need to import values into the Edge Table for them to be used as edge weights.
 2. Yes. You can use Layout > Node Layout Tools. Or you can use Layout > Settings… to tune the parameters on the particular layout algorithm you are using. I almost always tune a layout, rather than relying on arbitrary default values.

 - Alex



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Alex Pico

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Jul 28, 2019, 2:03:13 PM7/28/19
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Your question was selected for this month's feature demo video showing how to tune layout parameters using Layout > Settings...


Enjoy!
  - Alex

On Sunday, June 16, 2019 at 11:52:47 AM UTC-7, Alex Pico wrote:
Hi Sandra,

You’ve hit upon two of the most common uses for Cytoscape: data mapping (i.e., using data values to control visual properties) and layout. There are a ton of features related to these types of operations. I recommend starting with one of our tutorials:

Browse the other tutorials there as well and check out some of the videos at:

There is a video for example on layouts and how to “spread out” nodes using Node Layout Tools: 

To address your specific questions:
 1A. Some layouts support using attribute values. See "Edge-weighted …” layouts in the Layout menu
 1B. P-value on fold changes sounds like a node-based measure. You’ll need to import values into the Edge Table for them to be used as edge weights.
 2. Yes. You can use Layout > Node Layout Tools. Or you can use Layout > Settings… to tune the parameters on the particular layout algorithm you are using. I almost always tune a layout, rather than relying on arbitrary default values.

 - Alex



On Jun 16, 2019, at 11:30 AM, sandra yin <sandr...@gmail.com> wrote:

Hi, 

Thanks in advance for your help. 
After I put in my network dataset, it generated this interaction map. 
Two questions: 
1. Do the length of the line or size of the node correspond to any quantitative information I put in? I did have p-value and fold change in my table. 
2. Is there a convenient way to make the entire interaction map more spread out, so that the nodes don't overlap?

Thank you very much. 


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