User Community
cancel
Turn on suggestions
Auto-suggest helps you quickly narrow down your search results by suggesting possible matches as you type.
Showing results for 
Show  only  | Search instead for 
Did you mean: 
  • Instantly extract effect sizes, F-ratios, and FDR-adjusted p-values from your models with the Calculate Effects Sizes extension, available now in the JMP Marketplace!
  • New to JMP? Join us Sept. 23-24 for the Early User Edition of Discovery Summit, tailor-made for new users. Register now for free!
  • See how to use the JMP Marketplace – Free tools to expand JMP capabilities. Register. July 10, 2 pm US Eastern Time.

Discussions

Solve problems, and share tips and tricks with other JMP users.
Choose Language Hide Translation Bar
salihkafkas
salihkafkas
Level I

circos plot

Oct 9, 2018 04:41 AM (4913 views)

Does anyone know how to make a circos plot for synteny analysis using JMP Genomics?

0 Kudos
1 ACCEPTED SOLUTION

Accepted Solutions
Chris_Kirchberg
Staff Chris_Kirchberg
Staff
Solution

Re: circos plot

Oct 9, 2018 04:11 PM (4876 views)  |  Posted in reply to message from salihkafkas 10-09-2018

Hello,

 

It is possible. To make one, use the Genome Browswer under Genome Views.  Here is a link to the documentation:

 

https://www.jmp.com/support/downloads/JMPG90_documentation/wwhelp/wwhimpl/js/html/wwhelp.htm#href=ST...

 

The key will be to use the Link Tab in the dialog for this process. Here is a link with a couple more details:

 

http://www.jmp.com/support/downloads/JMPG90_documentation/wwhelp/wwhimpl/js/html/wwhelp.htm#href=PA_...

 

A good example of what you will need is shown by clicking on the "Load" button at the bottom of the dialog and chosing the AffyHuEx1Circular example settings.  This will show some example settings and an example Links SAS Input Data Set that you can open to see what you will need to make the links between the chromosomes.

 

If you need more, you might want to contact [email protected].

 

Thanks,

 

Chris Kirchberg

Chris Kirchberg, M.S.2
Data Scientist, Life Sciences - Global Technical Enablement
JMP Statistical Discovery, LLC. - Denver, CO
Tel: +1-919-531-9927 ▪ Mobile: +1-303-378-7419 ▪ E-mail: [email protected]
www.jmp.com

View solution in original post

1 REPLY 1
Chris_Kirchberg
Staff Chris_Kirchberg
Staff
Solution

Re: circos plot

Oct 9, 2018 04:11 PM (4877 views)  |  Posted in reply to message from salihkafkas 10-09-2018

Hello,

 

It is possible. To make one, use the Genome Browswer under Genome Views.  Here is a link to the documentation:

 

https://www.jmp.com/support/downloads/JMPG90_documentation/wwhelp/wwhimpl/js/html/wwhelp.htm#href=ST...

 

The key will be to use the Link Tab in the dialog for this process. Here is a link with a couple more details:

 

http://www.jmp.com/support/downloads/JMPG90_documentation/wwhelp/wwhimpl/js/html/wwhelp.htm#href=PA_...

 

A good example of what you will need is shown by clicking on the "Load" button at the bottom of the dialog and chosing the AffyHuEx1Circular example settings.  This will show some example settings and an example Links SAS Input Data Set that you can open to see what you will need to make the links between the chromosomes.

 

If you need more, you might want to contact [email protected].

 

Thanks,

 

Chris Kirchberg

Chris Kirchberg, M.S.2
Data Scientist, Life Sciences - Global Technical Enablement
JMP Statistical Discovery, LLC. - Denver, CO
Tel: +1-919-531-9927 ▪ Mobile: +1-303-378-7419 ▪ E-mail: [email protected]
www.jmp.com

Recommended Articles