Compensate data using values stored in spill

Usage

spillover.apply(flowstate.object, decompensate = FALSE)

Arguments

flowstate.object: the return of read.flowstate.
decompensate: Logical; if TRUE, will return data values to their original state.

Value

Updated flowstate$data; !!!updates by reference – no assignment.

Examples

fcs.file.paths <- system.file("extdata", package = "flowstate") |>
list.files(full.names = TRUE, pattern = "BLOCK.*.fcs")

#read all .fcs files as flowstate objects; concatenate into a single object
fs <- read.flowstate(
  fcs.file.paths,
  colnames.type="S",
  concatenate = TRUE
)
#> COVAIL_002_CYTOKINE_BLOCK1_1.fcs --> flowstate
#> COVAIL_002_CYTOKINE_BLOCK1_2.fcs --> flowstate
#> COVAIL_002_CYTOKINE_BLOCK1_3.fcs --> flowstate
#> Concatenating 'flowstate.ojects'...

#transform
flowstate.transform(fs,c('CD4','CD8'))
#> flowstate.object --> transforming...

#row index; CD4 vs CD8
index<-which(names(fs$spill) %in% c('CD4','CD8'))

#update a spill value
spillover.update.value(fs,CD8,CD4,0.03)

#over-compensated data
plot(fs,CD4,CD8) + ggplot2::labs(title = "Over-compensated")
#> Warning: Computation failed in `stat_binhex()`.
#> Caused by error in `compute_group()`:
#> ! The package "hexbin" is required for `stat_bin_hex()`.


#apply compensation
spillover.apply(fs)
#> flowstate.object --> transforming...

#compensated data
plot(fs,CD4,CD8) + ggplot2::labs(title = "Compensated")
#> Warning: Computation failed in `stat_binhex()`.
#> Caused by error in `compute_group()`:
#> ! The package "hexbin" is required for `stat_bin_hex()`.


#return data values to original state by decompensating
spillover.apply(fs,decompensate=TRUE)
#> flowstate.object --> transforming...

plot(fs,CD4,CD8) + ggplot2::labs(title = "Over-compensated")
#> Warning: Computation failed in `stat_binhex()`.
#> Caused by error in `compute_group()`:
#> ! The package "hexbin" is required for `stat_bin_hex()`.