add useNormFilt = FALSE to tests to reflect bugfix

RGLab · Dec 16, 2021 · d54ac0a · d54ac0a
1 parent 5323bb0
commit d54ac0a
Showing 1 changed file with 17 additions and 9 deletions.
diff --git a/tests/testthat/test-spillover.R b/tests/testthat/test-spillover.R
@@ -17,7 +17,9 @@ controls <- controls[,c(3,1,4,5,2,6,7)]
 test_that("spillover: Match columns using regexpr", {
   ref_file <- system.file("extdata", "compdata", "compref1", package="flowCore")
   comp_ref <- as.matrix(read.table(ref_file, check.names = FALSE))
-  comp <- spillover(controls, unstained = "UNSTAINED", fsc="FSC-H", ssc="SSC-H", patt = "-H", stain_match="regexpr")
+  comp <- spillover(controls, unstained = "UNSTAINED", fsc="FSC-H",
+                    ssc="SSC-H", patt = "-H", stain_match="regexpr",
+                    useNormFilt = FALSE)
   expect_equal(colnames(comp), colnames(comp_ref))
   expect_equal(rownames(comp), rownames(comp_ref))
   expect_equivalent(comp, comp_ref, tolerance=3e-08)
@@ -28,7 +30,9 @@ test_that("spillover: Match columns using ordered", {
   comp_ref <- as.matrix(read.table(ref_file, check.names = FALSE))
   # The spillover matrix here should (appropriately) be incorrect bc the rows are
   # not in the order of the columns.
-  comp <- spillover(controls, unstained = "UNSTAINED", fsc="FSC-H", ssc="SSC-H", patt = "-H", stain_match="ordered")
+  comp <- spillover(controls, unstained = "UNSTAINED", fsc="FSC-H",
+                    ssc="SSC-H", patt = "-H", stain_match="ordered",
+                    useNormFilt = FALSE)
   expect_equal(colnames(comp), colnames(comp_ref))
   expect_equal(rownames(comp), rownames(comp_ref))
   expect_equivalent(comp, comp_ref, tolerance=3e-08)
@@ -37,19 +41,20 @@ test_that("spillover: Match columns using ordered", {
 test_that("spillover: Match columns using intensity", {
   ref_file <- system.file("extdata", "compdata", "compref1", package="flowCore")
   comp_ref <- as.matrix(read.table(ref_file, check.names = FALSE))
-  comp <- spillover(controls, unstained = "UNSTAINED", fsc="FSC-H", ssc="SSC-H", patt = "-H", stain_match="intensity")
+  comp <- spillover(controls, unstained = "UNSTAINED", fsc="FSC-H",
+                    ssc="SSC-H", patt = "-H", stain_match="intensity",
+                    useNormFilt = FALSE)
   expect_equal(colnames(comp), colnames(comp_ref))
   expect_equal(rownames(comp), rownames(comp_ref))
   expect_equivalent(comp, comp_ref, tolerance=3e-08)
 })
 
-
 test_that("spillover_match: Using path to dir with files", {
   ref_file <- system.file("extdata", "compdata", "compref3", package="flowCore")
   comp_ref <- as.matrix(read.table(ref_file, check.names = FALSE))
   matched <- spillover_match(path=control_path, fsc="FSC-H", ssc="SSC-H", matchfile = matchfile_path)
   comp <- spillover(matched, prematched = TRUE, fsc="FSC-H", ssc="SSC-H", patt = "-H",
-                    useNormFilt = TRUE, method = "mode")
+                    useNormFilt = FALSE, method = "mode")
   expect_equal(colnames(comp), colnames(comp_ref))
   expect_equal(rownames(comp), rownames(comp_ref))
   expect_equivalent(comp, comp_ref, tolerance=3e-08)
@@ -61,7 +66,7 @@ test_that("spillover_match: Using preconstructed flowSet with filenames as sampl
   comp_ref <- as.matrix(read.table(ref_file, check.names = FALSE))
   matched <- spillover_match(controls, fsc="FSC-H", ssc="SSC-H", matchfile = matchfile_path)
   comp <- spillover(matched, prematched = TRUE, fsc="FSC-H", ssc="SSC-H", patt = "-H",
-                    useNormFilt = TRUE, method = "mode")
+                    useNormFilt = FALSE, method = "mode")
   expect_equal(colnames(comp), colnames(comp_ref))
   expect_equal(rownames(comp), rownames(comp_ref))
   expect_equivalent(comp, comp_ref, tolerance=3e-08)
@@ -71,7 +76,8 @@ test_that("spillover_ng: Using path to dir with files", {
   ref_file <- system.file("extdata", "compdata", "compref4", package="flowCore")
   comp_ref <- as.matrix(read.table(ref_file, check.names = FALSE))
   comp <- spillover_ng(path=control_path, fsc="FSC-H", ssc="SSC-H", 
-                       patt="-H", matchfile = matchfile_path, pregate = FALSE)
+                       patt="-H", matchfile = matchfile_path, pregate = FALSE,
+                       useNormFilt = FALSE)
   expect_equal(colnames(comp), colnames(comp_ref))
   expect_equal(rownames(comp), rownames(comp_ref))
   expect_equivalent(comp, comp_ref, tolerance=3e-08)
@@ -83,7 +89,8 @@ test_that("spillover_ng: Using preconstructed flowSet with filenames as sample n
   comp_ref <- as.matrix(read.table(ref_file, check.names = FALSE))
   matched <- spillover_match(controls, fsc="FSC-H", ssc="SSC-H", matchfile = matchfile_path)
   comp <- spillover_ng(path=control_path, fsc="FSC-H", ssc="SSC-H", 
-                       patt="-H", matchfile = matchfile_path, pregate = FALSE)
+                       patt="-H", matchfile = matchfile_path, pregate = FALSE,
+                       useNormFilt = FALSE)
   expect_equal(colnames(comp), colnames(comp_ref))
   expect_equal(rownames(comp), rownames(comp_ref))
   expect_equivalent(comp, comp_ref, tolerance=3e-08)
@@ -104,7 +111,8 @@ test_that("spillover_ng: Using preconstructed flowSet with channels in new order
   # approach used to re-order rows of the matrix in the spillover function.
 
   comp <- spillover_ng(x=fs, fsc="FSC-H", ssc="SSC-H", 
-                       patt="-H", matchfile = matchfile_path, pregate = FALSE)
+                       patt="-H", matchfile = matchfile_path, pregate = FALSE,
+                       useNormFilt = FALSE)
   # The diagonals should be equal to 1
   for (i in 1:4) {
     expect_equal(comp[i,i], 1)