How to run a list of genes with lollipop plot?

[Yang Sui]

Hi,

Thank you for developing the tool~ I used this tool a lot last year, and I was wondering if there is a way to upload a file with variants in multiple genes and create lollipop plots for each of these genes~

Another question is if you plan to do any lollipop plots for variants in the non-coding regions? 

Thanks,

Kate

[Karishma Gangwani]

Hi Yang,

Thanks for reaching out to us with your questions. You can add additional variants by clicking the '+' button next to the datasets as shown below. and then select the type of position you want to add (whether codon, genomic or RNA), and you can visualize the details for the specific categories. I have added a test example (just hypothetical) for you to see. Hope that helps. Let us know if you have any more questions.

Thanks for using ProteinPaint.

Best Regards,

Karishma Gangwani

Ph.D. Biology

Computational Biology Department
St Jude Children's Research Hospital

LinkedIn

Github
Contently

Twitter

Website

Pronouns She/Her/Hers

--
You received this message because you are subscribed to the Google Groups "ProteinPaint" group.
To unsubscribe from this group and stop receiving emails from it, send an email to proteinpaint...@googlegroups.com.
To view this discussion visit https://groups.google.com/d/msgid/proteinpaint/893e3c42-bda6-4f82-9def-d8a511913bbfn%40googlegroups.com.

[Yang Sui]

Hi Karishma,

 

Thank you for getting back to me~

 

I have used this tool for two years and have no problem loading the variants in a certain gene~
My previous question might be confusing~ And I would like to rephrase it and provide an old example, please see detailed description below,

Previously, there was an option to input multiple files like this “testA”:

Then, if I choose one gene, like CAMTA1, one track should be “testA”, and the other tracks would be named as “testB”, “testC” and etc.
In this case, I can get 8 lollipop plots for each of these 8 genes (column “gene”), and within each of the plot, I have different tracks.

This is still the ideal output I want. But based on the current version, I didn’t see any option on the website. I was wondering if this option/function exists or not, and if there is another way or command line to do it~ It would be super useful to allow us to generate figures for multiple genes with different tracks at the same time~

Please feel free to let me know if you have any questions, and I’m looking forward to hearing from you!

Thanks,

Yang

 

From: protei...@googlegroups.com <protei...@googlegroups.com> on behalf of Karishma Gangwani <karishma....@gmail.com>
Date: Tuesday, January 28, 2025 at 9:20 PM
To: Yang Sui <yan...@uw.edu>
Cc: ProteinPaint <protei...@googlegroups.com>
Subject: Re: How to run a list of genes with lollipop plot?

Hi Yang, Thanks for reaching out to us with your questions. You can add additional variants by clicking the '+' button next to the datasets as shown below. and then select the type of position you want to add (whether codon, genomic

ZjQcmQRYFpfptBannerStart

This Message Is From an Untrusted Sender

You have not previously corresponded with this sender.

See https://itconnect.uw.edu/email-tags for additional information. Please contact the UW-IT Service Center, he...@uw.edu 206.221.5000, for assistance.

 

ZjQcmQRYFpfptBannerEnd

Hi Yang,

 

Thanks for reaching out to us with your questions. You can add additional variants by clicking the '+' button next to the datasets as shown below. and then select the type of position you want to add (whether codon, genomic or RNA), and you can visualize the details for the specific categories. I have added a test example (just hypothetical) for you to see. Hope that helps. Let us know if you have any more questions.

 

Thanks for using ProteinPaint.

 

 

Best Regards,

Karishma Gangwani

Ph.D. Biology

Computational Biology Department
St Jude Children's Research Hospital

LinkedIn

Github
Contently

Twitter

Website

 

Pronouns She/Her/Hers

 

 

On Tue, Jan 28, 2025 at 8:15 PM Yang Sui <yan...@uw.edu> wrote:

Hi,

 

Thank you for developing the tool~ I used this tool a lot last year, and I was wondering if there is a way to upload a file with variants in multiple genes and create lollipop plots for each of these genes~

Another question is if you plan to do any lollipop plots for variants in the non-coding regions? 

 

Thanks,

Kate

--
You received this message because you are subscribed to the Google Groups "ProteinPaint" group.
To unsubscribe from this group and stop receiving emails from it, send an email to proteinpaint...@googlegroups.com.
To view this discussion visit https://groups.google.com/d/msgid/proteinpaint/893e3c42-bda6-4f82-9def-d8a511913bbfn%40googlegroups.com.

--
You received this message because you are subscribed to a topic in the Google Groups "ProteinPaint" group.
To unsubscribe from this topic, visit https://groups.google.com/d/topic/proteinpaint/6ZlSeocS_oA/unsubscribe.
To unsubscribe from this group and all its topics, send an email to proteinpaint...@googlegroups.com.
To view this discussion visit https://groups.google.com/d/msgid/proteinpaint/CAOXfWhBmiCLYKYqZhxO90893EuSpE%3DiR9H3d3eK15fE4MTWPww%40mail.gmail.com.

[Karishma Gangwani]

Hi Yang,

Thanks for providing that explanation. We do have a way such that a user can host their data file from their local system. For that ProteinPaint would have to be installed locally on your system. 

We are currently working on a fix for that so I will get back to you as soon as we have a better solution for you. Apologies we are unable to resolve your request on an immediate basis. But in the meantime, the option I showed you previously should work. 

Best,
Karishma Sanjay Gangwani, PhD
SJCRH

[Yang Sui]

Hi Karishma,

 

Thank you for the information, and efficiently generating tons of figures using one cmd would be super helpful for users like me.
I would love to install it on my system whenever you have it.

Thank you again for all your efforts.

 

Thanks,

Yang

 

From: Karishma Gangwani <karishma....@gmail.com>
Date: Wednesday, January 29, 2025 at 12:50 PM
To: Yang Sui <yan...@uw.edu>
Cc: ProteinPaint <protei...@googlegroups.com>
Subject: Re: How to run a list of genes with lollipop plot?

Hi Yang, Thanks for providing that explanation. We do have a way such that a user can host their data file from their local system. For that ProteinPaint would have to be installed locally on your system. We are currently working on a fix for