Better checks

[ellispatrick]

No error is thrown if the image ID is not in the data.

Non helpful errors are thrown if the transformations are incorrect (sinh instead of asinh).

[fame2827]

If imageID is not in the data or misspecified, simpleSeg will run normally but not perform any transformations which require imageID to be specified e.g. trim99, minMax and mean.

Example:

testSCE = simpleSeg::normalizeCells(
  cells = testSCE,
  assayIn = "intensities",
  assayOut = "norm",
  imageID = "column_that_doesn't_exist",
  method = c("trim99", "minMax")
)

# Original marker intensities
assay(testSCE, "intensities")[rownames(testSCE)[[1]], ] |> 
  density() |> 
  plot()

# Normalised marker intensities
assay(testSCE, "norm")[rownames(testSCE)[[1]], ] |> 
  density() |> 
  plot()

The above code outputs the same plot when the second plot should be normalised.