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stemangiola / cellsig

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Implement shiny app in the WEHI servers #66

Closed stemangiola closed 1 year ago

stemangiola commented 2 years ago
stemangiola commented 2 years ago

Here the original app was pulled off the remote server because nobody could conclude the implementation.

/stornext/Bioinf/data/bioinf-data/Papenfuss_lab/projects/app_for_Kamran/ShinyApps

Kamran-Khan96 commented 2 years ago

Hi @stemangiola,

Apologies for the delayed response.

I have some queries-

  1. Should I scale and Impute the missing abundances using hierarchical approach to generate the expression data frame?

  2. It's not clear how Jian previously generated the PC values. Should I use the whole data for PCA and generating the PC values?

  3. Should I request for the hosting of the app? or you should do it? Does it need to be done now or we can do it after checking it out locally?

Cheers, Kamran

stemangiola commented 2 years ago
  1. Should I scale and Impute the missing abundances using hierarchical approach to generate the expression data frame?

scale yes impute no, there will be some genes will fewer data, which is the reality.

2. It's not clear how Jian previously generated the PC values. Should I use the whole data for PCA and generating the PC values?

You should use the signature genes

3. Should I request for the hosting of the app? or you should do it? Does it need to be done now or we can do it after checking it out locally?

Do things in parallel, proceed with request and test locally at the same time.

Kamran-Khan96 commented 2 years ago

scale yes impute no, there will be some genes will fewer data, which is the reality.

You should use the signature genes

Do things in parallel, proceed with request and test locally at the same time.

  • Understood
stemangiola commented 2 years ago
  • Which set of signature genes to use? As you know I currently have multiple sets of signature genes (a bunch from the cibersortx (of different sizes) and 1 from non-hierarchical cellsig)

The one that gives the best PCA. For the sake of development don;t spend too much time on this choice.

Kamran-Khan96 commented 2 years ago

The one that gives the best PCA. For the sake of development don;t spend too much time on this choice.

ok, understood!

Kamran-Khan96 commented 2 years ago

Updated files for testing the app have been uploaded here- https://github.com/stemangiola/cellsig/tree/updated_shiny_app_files/dev/shiny_kamran/ShinyApps/shiny_pub/v2

stemangiola commented 2 years ago

Thanks. Is any way we can see the shiny app live?

Kamran-Khan96 commented 2 years ago

Thanks. Is any way we can see the shiny app live?

  • Yes if we want to see it live locally.
  1. You can just switch to the branch "updated_shiny_app_files" and locate the "app_v2.R" file and open it.
  2. Then simply just run the app. image
  3. Then you can just open it on browser and navigate as necessary. image
Kamran-Khan96 commented 2 years ago

@stemangiola ,

Do you want me to publish it on shinyapps.io? If we publish it here, maybe It'll be open for everyone. I'm not sure.

stemangiola commented 2 years ago

@stemangiola ,

Do you want me to publish it on shinyapps.io? If we publish it here, maybe It'll be open for everyone. I'm not sure.

Are you able to publish on WEHI servers? How complicated is it to publish - edit - and publish again?

What would the public URL be of that WEHI app?

Kamran-Khan96 commented 2 years ago

Are you able to publish on WEHI servers?

Yes, as soon as they finish processing my request and allocate me a space. So, I can not publish this until that.

How complicated is it to publish - edit - and publish again?

It should be fairly easy. I just need to transfer the files to the app directory. I think you can simply update the files and your app.R data as many times as you want, you just need to replace the old files.

What would the public URL be of that WEHI app?

If we look at Julie's example, it should look something like- https://shiny.wehi.edu.au/iskander.j/testapp/

You can see the details from here- https://wehieduau.sharepoint.com/sites/rc2/SitePages/Setting-up-Shiny-app.aspx

stemangiola commented 2 years ago

Maybe at this stage, it would be worth publishing it on WEHI, so I can give feedback on the actual website.

Kamran-Khan96 commented 2 years ago

Maybe at this stage, it would be worth publishing it on WEHI, so I can give feedback on the actual website.

Ok, so we have to wait for the access then. And yes, I lot can vary between the local hosting and web-hosting. If you have any suggestion on anything (by looking at the local-hosting, as it'll be essentially the same), let me know.

Kamran-Khan96 commented 1 year ago

Resolved