Hi All,

I am attempting to use the plotPlatePosition function in scater and having some issues with it. Specifically, I have a 96-well plate where the data are incomplete. I have "Cell.Position" as metadata data added to my sce object using colData() where locations are listed as A1, A2, A12, B2, B10, etc... However, this standard 96-well plate (rows A-H, columns 1-12) is missing cells. This is what I've tried:

# subseting my plate of interest, here Plate3 (this plate has 72 wells, therefore missing some positions)
example_sce2 <- subset(example_sce1, , Plate.Name=="Plate3")

# defining plate position as a 96-well plate
example_sce2$plate_position <- paste0(
  rep(LETTERS[1:8], each = 12),
  rep(formatC(1:12, width = 2, flag = "0"), 8))

Error in `[[<-`(`*tmp*`, name, value = c("A01", "A02", "A03", "A04", "A05",  :
  96 elements in value to replace 72 elements

# when I try running the following either after above or before, I get the same error
plotPlatePosition(example_sce2, colour_by = "total_counts")

Error in `[[<-`(`*tmp*`, name, value = c("A01", "A02", "A03", "A04", "A05",  :
  96 elements in value to replace 72 elements

If I replace the 96-well plate in plate_position to create a 72 well plate here by doing letters[1:6], it generates a plate plot with A-F instead of A-H that does not show original position of cells. Is there a way for "ignoring" the empty/unlisted positions in a 96-well plate?

Thank you in advance for all of your help!

Your question suggests some fundamental misunderstandings about how this works. example_sce2 only has 72 columns, so why are you trying to assign a vector with 96 elements to plate_position in the column data? Moreover, it's incorrect to subset LETTERS - as you've found out, just because you get a vector of the same length doesn't mean that the well identities are correct. And obviously, if you tell plotPlatePosition that the first library is at A1, then that's what it'll plot - what else could it do? 

You should have the relevant metadata for your experiment available somewhere. Load it from file, match up the rows of the metadata to the identity and ordering of columns in your SCE object, and use the matched values to populate the colData fields including plate_position.