Spectral detection needs more than one raw detector, and the keep rule matches the detection's case

inst/app/R/fcs_import.R

@@ -328,16 +328,20 @@ filter_flow_channels <- function(ff) {
   # rather than the detector — $PnN "FL1-A" with $PnS "FITC-A" — satisfies it on every
   # fluorescence channel while having no detectors at all, and filtering it drops the
   # height partners and any spelled-out width. Beckman CytoFLEX lost 5 of 14 channels
-  # this way and Xitogen XTG-1600 lost 14 of 32. So also require at least one channel
-  # the filter would actually drop: not scatter, not LightLoss/Autofluorescence/
-  # Extinction, not QC/timing, and carrying no marker of its own.
+  # this way and Xitogen XTG-1600 lost 14 of 32. So also require channels the filter
+  # would actually drop -- not scatter, not LightLoss/Autofluorescence/Extinction, not
+  # QC/timing, and carrying no marker of its own -- and more than one of them: a
+  # conventional file with a single unlabelled fluorescence channel (an unstained or
+  # spare detector) was taken for a spectral one, which dropped its height and width
+  # channels and changed every gate's channel identity between files of one panel. A
+  # spectral file carries dozens. GateLab's channels.ts applies the same rule.
   has_marker <- !is.na(pns) & nchar(trimws(pns)) > 0 & pns != pnn
   is_raw_detector <- !has_marker &
     !grepl("^(FSC|SSC)", pnn, ignore.case = TRUE) &
     !grepl("^(LightLoss|Autofluorescence|Extinction)", pnn, ignore.case = TRUE) &
     !grepl("^(Time|Event_length|Cell_length)$", pnn, ignore.case = TRUE)
 
-  if (sum(is_unmixed) < 2 || !any(is_raw_detector)) {
+  if (sum(is_unmixed) < 2 || sum(is_raw_detector) < 2) {
     display_name <- ifelse(is.na(pns) | nchar(trimws(pns)) == 0, pnn, pns)
     message("  Conventional flow: keeping all ", length(pnn), " channels")
     return(list(ff = ff, display_names = display_name,
@@ -382,9 +386,11 @@ filter_flow_channels <- function(ff) {
       next
     }
 
-    # Unmixed fluorophore channels: PnS != PnN AND PnS ends with "-A"
+    # Unmixed fluorophore channels: PnS != PnN AND PnS ends with "-A". Case-insensitive, as
+    # the detection above is: a marker written "-a" counted towards making the file unmixed
+    # and then fell through to the drop branch here, losing the channel.
     if (!is.na(desc) && nchar(trimws(desc)) > 0 &&
-        desc != ch && grepl("-A$", desc)) {
+        desc != ch && grepl("-A$", desc, ignore.case = TRUE)) {
       keep_idx[i] <- TRUE
       display_name[i] <- paste0(desc, " (", ch, ")")
       pnr_out[i] <- pnr[i]

tests/testthat/test-channel-identities.R

@@ -59,13 +59,14 @@ test_that("conjugate names ending -A do not make a file spectral-unmixed", {
   unlink(path)
 })
 
-test_that("a raw detector alongside unmixed markers still triggers filtering", {
+test_that("raw detectors alongside unmixed markers still trigger filtering", {
   skip_if_not_installed("flowCore")
 
-  # Same file plus one raw spectral detector (no $PnS of its own). That is what an
-  # unmixed export looks like, so the detector is dropped and markers are renamed.
-  chans <- c("FSC-A", "B1-A", "V500-A", "PE-A")
-  descs <- c("FSC-A", NA, "CD4-A", "CD25-A")
+  # Same file plus raw spectral detectors (no $PnS of their own). That is what an unmixed
+  # export looks like, so the detectors are dropped and markers are renamed. A marker written
+  # "-a" is an unmixed marker too, in the keep rule as in the detection.
+  chans <- c("FSC-A", "B1-A", "B2-A", "V500-A", "PE-A")
+  descs <- c("FSC-A", NA, NA, "cd4-a", "CD25-A")
   values <- matrix(seq_len(3 * length(chans)), nrow = 3,
                    dimnames = list(NULL, chans))
   frame <- flowCore::flowFrame(values)
@@ -76,7 +77,30 @@ test_that("a raw detector alongside unmixed markers still triggers filtering", {
   sce <- import_fcs_files(path, instrument_mode = "flow")
 
   expect_false("B1-A" %in% rownames(sce))
-  expect_identical(rownames(sce), c("FSC-A", "CD4-A (V500-A)", "CD25-A (PE-A)"))
+  expect_false("B2-A" %in% rownames(sce))
+  expect_identical(rownames(sce), c("FSC-A", "cd4-a (V500-A)", "CD25-A (PE-A)"))
+
+  unlink(path)
+})
+
+test_that("one unlabelled fluorescence channel does not make a conventional file spectral", {
+  skip_if_not_installed("flowCore")
+
+  # An unstained or spare channel on a conventional analyser: one channel without $PnS. It
+  # used to count as the raw detector that makes a file spectral-unmixed, which dropped every
+  # -H channel and changed the gate channel identities between files of one panel.
+  chans <- c("FSC-A", "FL1-H", "FL1-A", "FL2-H", "FL2-A", "FL3-A")
+  descs <- c("FSC-A", "FITC-H", "FITC-A", "PE-H", "PE-A", NA)
+  values <- matrix(seq_len(3 * length(chans)), nrow = 3,
+                   dimnames = list(NULL, chans))
+  frame <- flowCore::flowFrame(values)
+  flowCore::pData(flowCore::parameters(frame))$desc <- descs
+  path <- tempfile(fileext = ".fcs")
+  flowCore::write.FCS(frame, path)
+
+  sce <- import_fcs_files(path, instrument_mode = "flow")
+
+  expect_identical(rownames(sce), c("FSC-A", "FITC-H", "FITC-A", "PE-H", "PE-A", "FL3-A"))
 
   unlink(path)
 })