pass value for cutoff (#754)

Signed-off-by: Daena Rys <rysdaena8@gmail.com>

Author: 0xMuluh

R/transformCounts.R

@@ -48,8 +48,11 @@
 #'   specifies relative difference threshold and determines the first point
 #'   where the relative change in  differences between consecutive quantiles
 #'   exceeds this threshold. (Default: \code{0.1}) For \code{"cutoff"},
-#'   values less than or equal to the threshold are replaced with \code{NA}.
+#'   values less than or equal to the threshold are replaced with \code{value}.
 #'   (Default: \code{0})
+#'   \item \code{value}: \code{Numeric scalar}. For  \code{"cutoff"}, specifies
+#'   the replacement value for counts less than or equal to the threshold. 
+#'   (Default: \code{NA})
 #'   \item \code{tree}: \code{phylo}. Phylogeny used in PhILR transformation.
 #'   If \code{NULL}, the tree is retrieved from \code{x}.
 #'   (Default: \code{NULL}).
@@ -102,7 +105,7 @@
 #'
 #' \item 'cutoff': In some ecological studies, only strictly positive values
 #' are taken into account. This method keeps only values greater than
-#' \code{threshold} and replaces all other values with \code{NA}.
+#' \code{threshold} and replaces all other values with \code{value}.
 #'
 #' }
 #'
@@ -813,10 +816,13 @@ setMethod("transformAssay", signature = c(x = "SingleCellExperiment"),
 }
 
 # This function replaces values under or equal to threshold with NA
-.apply_cutoff <- function(mat, threshold = 0, ...){
+.apply_cutoff <- function(mat, threshold = 0, value = NA, ...){
     if( !.is_a_numeric(threshold) ){
-        stop("'threshold' must be a single numierc value.", call. = FALSE)
+        stop("'threshold' must be a single numeric value.", call. = FALSE)
+    }
+    if( length(value) != 1L || (!is.numeric(value) && !is.na(value)) ){
+        stop("'value' must be a single numeric value or NA.", call. = FALSE)
     }
-    mat[ mat <= threshold ] <- NA
+    mat[ mat <= threshold ] <- value
     return(mat)
 }

man/transformAssay.Rd

@@ -405,6 +405,23 @@ test_that("transformAssay", {
             check.attributes = FALSE
         )
         expect_equal(colData(tse), colData(altExp(tse, "philr")))
+        ################################# CUTOFF ###############################
+        # Basic cutoff with NA value
+        expect_identical(
+            .apply_cutoff(c(0, 1, 2, 3, 0.5), 1), 
+            c(NA, NA, 2, 3, NA)
+        )
+        # Basic cutoff with numeric replacement
+        expect_identical(
+            .apply_cutoff(c(0, 1, 2, 3, 0.5), 2, value = 999), 
+            c(999, 999, 999, 3, 999)
+        )
+        # Error on non-length-1 value
+        expect_error(
+            .apply_cutoff(c(1, 2, 3), 1, value = c(1, 2)),
+            "'value' must be a single numeric value or NA"
+        )
+        
     }
 
     # TSE object