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how to load STpipeline output to semla #32

Open psecekartal opened 1 month ago

psecekartal commented 1 month ago

Hello I have 10X visium data which I have been using STutility to analyse so far. I want to switch to semla. However my dataset was analyzed not with spaceranger but with STpipeline. I dont have the same result files including .json files with scale factor info. When I create a vector for scale factor and give it infoTable, it doesn't accept it. Is there a solution to this?

infoTable <- tibble(samples, imgs, spotfiles, scalefactor, slide_id, sample, permeabilization, section_id, orig.ident, stringsAsFactors = F) sobj <- ReadVisiumData(infoTable = infoTable)

── Reading 10x Visium data ──

Error in select(): ℹ In argument: all_of(c("samples", "imgs", "spotfiles", "json")). Caused by error in all_of(): ! Can't subset elements that don't exist. ✖ Element json doesn't exist. Backtrace:

  1. semla::ReadVisiumData(infoTable = infoTable)
    1. tidyselect::all_of(c("samples", "imgs", "spotfiles", "json"))
jemorlanes commented 1 month ago

Hello! Thanks for using the package :)

What are you giving in the scalefactor column if you do not have a .json file?