voltron with jupyter notebook

[smc9477]

Thank you for creating such a great tool.
I am trying to perform an analysis on a Jupyter Notebook using a conda environment as the kernel on a Linux server. However, the IP I can use is fixed, and it seems that the registerSpatialData function does not allow me to fix the IP. Additionally, due to server policies, I am unable to use RStudio.

Could you please suggest what I can do in this situation?

[Artur-man]

Hello there,

Thanks so much <3

Hmm perhaps I can configure the port where it can be an option for any function that requires shiny applications. As an alternative, if you wanna use VoltRon in a jupyter notebook (with R kernel?) perhaps we can trigger shiny using htmlwidgets which is supported in Jupyter notebooks. Would you also prefer that ?

[Artur-man]

I have pushed an update to the shiny-based routines to recognize options from the shinyApp function. Hence now you can pass information on host and port. Wanna give it a try?

annotateSpatialData(visium_data, shiny.options = list(host = "127.0.0.1", port = 6356))

vrSpatialPlot(visium_data, interactive = TRUE, shiny.options = list(port = 6356))

annotateSpatialData(visium_data, shiny.options = list(port = 6356))

registerSpatialData(reference_spatdata = visium_data, 
                    query_spatdata = visium_data, 
                    shiny.options = list(host = "127.0.0.1", port = 6356))

The update is on dev now. Please remove the R package, restart R session and download VoltRon from dev branch again to try.

[smc9477]

thank you for update function.

i've removed the R package and re-download from dev, but still there is no shiny.options at registerSpatialData function.
could you chek it? Thank you for your time

[Artur-man]

Hello there, I have just tried pulling from the dev branch to see if it is working, and it does:
devtools::install_github("BIMSBbioinfo/VoltRon@dev")

Reinstalling R packages are bit more tricky then it should be, you have to make sure that you deleted it by attemping to delete twice, and restart the R session before downloading, otherwise you get the same package ... also main branch still doesnt have the modification

[smc9477]

it worked successfully!! thank you so much for your effort!!
i reinstalled R package with deleting three times (<- it really worked)
i had been working with fuji, but it's much better.

[Artur-man]

It was my pleasure my friend, thanks for the feedback :D
Just one question though, is this automated registration or manual ?

[smc9477]

Yes i used automated registration!

[smc9477]

Hi again! Instead of manually interacting with the Shiny app, I want to automate the process and get the results directly in a single run.

Is there a way to convert the interactive steps that runs entirely in R with automated registration?

[Artur-man]

Hmm, we were thinking of implementing this as once you enter the correct parameters the run should just go through the alignment itself. We can implement this soon, will let know.

[Artur-man]

Hey there, we have an implementation for this now on the main branch. See also here.

There are some examples in the tutorials page now too.