In getFlowJoLabels(), if one of the cellTypes is not found in any…

… sample

of any group, issue warning instead of error, populates corresponding output
with NA's

NEWS.md

@@ -2,6 +2,9 @@
 
 ## CytoPipelineUtils 0.99.4
 - Added `getEventNbFromFJGates()`
+- In `getFlowJoLabels()`, if one of the `cellTypes` is not found in any sample 
+of any group, issue warning instead of error, populates corresponding output 
+with NA's
 
 ## CytoPipelineUtils 0.99.3
 - `applyFlowJoGate()` can now match sample file with sample names in wsp file,

R/gating.R

@@ -277,7 +277,7 @@ getFlowJoLabels <- function(ff,
   for (j in seq_along(cellTypes)) {
     if (!foundCellType[j]) {
       ct <- cellTypes[j]
-      stop("Cell type [", ct, "] not found in any sample of any group !")
+      warning("Cell type [", ct, "] not found in any sample of any group !")
     }
   }
 
@@ -292,10 +292,14 @@ getFlowJoLabels <- function(ff,
                        dimnames = list(NULL ,c(cellTypes, "unlabeled")))
 
   for (ct in cellTypes){
-    res$matrix[cellMap[[ct]], ct] <- TRUE
+      if (is.null(cellMap[[ct]])) {
+          res$matrix[, ct] <- NA
+      } else {
+          res$matrix[cellMap[[ct]], ct] <- TRUE
+      }
   }
 
-  res$matrix[, nCellTypes+1] <- (rowSums(res$matrix) == 0)
+  res$matrix[, nCellTypes+1] <- (rowSums(res$matrix, na.rm = TRUE) == 0)
 
 
   # 2. 'labels' with one label attached to each cell. If conflict, take the
@@ -308,7 +312,9 @@ getFlowJoLabels <- function(ff,
   }
 
   for (ct in cellTypes[order(nCellsByType, decreasing = TRUE)]) {
-    res$labels[cellMap[[ct]]] <- ct
+      if(!is.null(cellMap[[ct]])) {
+          res$labels[cellMap[[ct]]] <- ct
+      }
   }
 
   # 3. computed actualDiffTime (for withFJv10TimeCorrection work-around)

tests/testthat/test-gating.R

@@ -138,11 +138,21 @@ test_that("getFlowJoLabels works", {
     # what happens when cell type not found ?
     cellTypes <- c("Cells", "Debrais", "CD4+")
 
-    expect_error(getFlowJoLabels(agg,
+    expect_warning(resW <- getFlowJoLabels(agg,
                                  wspFile = wspFile,
                                  groups = groups,
                                  cellTypes = cellTypes),
-                 regexp = "not found in any sample of any group")
+                   regexp = "not found in any sample of any group")
+
+    labels <- resW$labels
+
+    expect_equal(sum(labels == "Cells"), 5518)
+    expect_equal(sum(labels == "CD4+"), 2552)
+    expect_equal(sum(labels == "Debrais"), 0)
+    expect_equal(sum(labels == "unlabeled"), 1930)
+
+    expect_equal(sum(resW$matrix[,"Cells"]), 8070)
+    expect_true(all(is.na(resW$matrix[,"Debrais"])))
 
     # with subset file from sample two only (special case where file 1 is not
     # represented in aggregate)