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prabhakarlab / Banksy

BANKSY: spatial clustering
https://prabhakarlab.github.io/Banksy
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missing code in multi-sample vignette page #19

Closed abraham-abin13 closed 8 months ago

abraham-abin13 commented 8 months ago

Hi, this seems like a great pipeline.

I was trying to reproduce the "Multi-sample analysis (10x Visium Human DLPFC)" vigneete.

In the "Running BANKSY" section, the variable spe_joint is not defined earlier in the code. I think you may be missing a line in the vigneete. I tried to replace spe_joint with spe_list from the above code section but got this error:

spe_joint <- runBanksyUMAP(spe_list, use_agf = use_agf, lambda = lambda, seed = 1000) Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘reducedDimNames’ for signature ‘"list"’

Thank you for your time!

jleechung commented 8 months ago

Hi @abraham-abin13 , thanks for catching this! There's a snippet of code that's not shown in the vignette - just add those lines and you should be able to run the rest of the code. We'll fix it soon.

jleechung commented 8 months ago

Fixed in c59f670