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jlab / FlowSoFineApp

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empty channels #7

Open sjanssen2 opened 2 years ago

sjanssen2 commented 2 years ago

image

What if I don't know which channels have been used for the experiment? For this example it was FSC-H and SSC-H, but assume I would erroneously select SCC-A. Currently this crashes the program with 

Transforming and subsetting flowSet
Warning in transformation(x@exprs[, channels]) : NaNs produced
Warning in transformation(x@exprs[, channels]) : NaNs produced
Warning in transformation(x@exprs[, channels]) : NaNs produced
Warning in transformation(x@exprs[, channels]) : NaNs produced
Warning in transformation(x@exprs[, channels]) : NaNs produced
Warning in transformation(x@exprs[, channels]) : NaNs produced
Warning in transformation(x@exprs[, channels]) : NaNs produced
Warning in transformation(x@exprs[, channels]) : NaNs produced
Warning in FSFTemplate(global$fcs, channels = input$channels, resolution = input$resolution,  :
  log transformations might shift events on the border because of events with an expression of 0. Consider using asinh instead.
Building coordinates for FSFtemplate with 2 dimensions and a resolution of 20 
Warning: Error in seq.default: 'from' must be a finite number
  2: shiny::runApp
  1: launchApp

on the console and no warning in the App

JonasKup commented 2 years ago

This is tough because often channels that weren't used to detect biological parameters still contain information so it wouldn't be easy to programmatically detect the correct ones. That selecting the wrong channel can crash the app is news to me though! I'll leave it open for now.

sjanssen2 commented 2 years ago

not sure if it is an actual crash, but the user does not see anything on the website other than it turning gray. We should somehow report this situation back to the user and suggest to change channels.