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prabhakarlab / Banksy

BANKSY: spatial clustering
https://prabhakarlab.github.io/Banksy
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object compute.banksymatrics not found #17

Closed alirezaah98 closed 9 months ago

alirezaah98 commented 9 months ago

hello, I have been trying to use Banksy on Xenium data and I have also tried to embed the coordinates inside the object but I still can't runBanksy function on ir because it lacks computebanksy matrics and apparently that function is not being run on Seurat object, so I was wondering if you could help me with it . Thanks

jleechung commented 9 months ago

Hi @alirezaah98, thanks for your interest in BANKSY and raising this issue. Could you please update your packages to the latest versions?

Install the feat-aft branch of our SeuratWrappers fork:

remotes::install_github('jleechung/seurat-wrappers@feat-aft')

Install the latest BANKSY version:

remotes::install_github('prabhakarlab/Banksy')
alirezaah98 commented 9 months ago

But still the problem persists even after updating the packages Fetching data from slot data from assay RNA Computing neighbor matrix Error in RunBanksy(wt_seurat, lambda = 0.2, dimx = "x", dimy = "x", assay = "Xenium", : object 'compute.banksyMatrices' not found

jleechung commented 9 months ago

Can you provide a minimal reproducible example, and print session information sessionInfo()?

alirezaah98 commented 9 months ago

Do I have to convert the Seurat object to Spatialexperiment object in order to run the algorithm?

jleechung commented 9 months ago

You can also do that, and follow the vignette here. Though, I'm curious why SeuratWrappers::RunBanksy doesn't work - the compute.banksyMatrices function should not be called. If you're willing to share your data, I'll be happy to troubleshoot it for you.

alirezaah98 commented 9 months ago

yeah , problem solved , perhaps just a bug in Rstudio, Thank you for your help