R/thermo-fisher.R

In priscian/volta: For Flow Cytometers, Calculate Minimum per-Channel Voltage for Optimal Resolution Sensitivity

## V. https://www.thermofisher.com/us/en/home/references/newsletters-and-journals/bioprobes-journal-of-cell-biology-applications/bioprobes-78/photomultiplier-tube-pmt-optimization-attune-nxt-flow-cytometer.html

#' @export
staining_index <- function(
  x, # Unused
  stain_groups,
  na.rm = FALSE,
  ...
)
{
  if (inherits(stain_groups, "findPeaks")) {
    diff(range(stain_groups$x)) / stain_groups["unstained", ]$w
  } else {
    negative <- stain_groups$unstained %>% unclass
    positive <- stain_groups$stained %>% unclass

    (stats::median(positive, na.rm = na.rm) - stats::median(negative, na.rm = na.rm)) /
      (2 * stats::sd(negative, na.rm = na.rm))
  }
}


#' @export
alt_staining_index <- function(
  x, # Unused
  stain_groups,
  na.rm = FALSE,
  ...
)
{
  if (inherits(stain_groups, "findPeaks")) {
    stain_groups["stained", ]$x / (stain_groups["unstained", ]$w / 2)
  } else {
    negative <- stain_groups$unstained %>% unclass
    positive <- stain_groups$stained %>% unclass

    stats::median(positive, na.rm = na.rm) / stats::sd(negative, na.rm = na.rm)
  }
}


#' @export
voltration_index <- function(
  x, # Unused
  stain_groups,
  quantity,
  na.rm = FALSE,
  ...
)
{

  ## Staining Index (SI)
  #si <- staining_index(NULL, stain_groups)

  ## Alternative Staining Index (Alt SI)
  alt_si <- staining_index(NULL, stain_groups, ...)

  vi <- alt_si / sqrt(quantity)

  vi
}