test-featureSelection fixed

compbiomed · Jan 29, 2024 · bbdcc35 · bbdcc35
1 parent 515115c
commit bbdcc35
Show file tree

Hide file tree

Showing 2 changed files with 18 additions and 18 deletions.
diff --git a/R/plotTopHVG.R b/R/plotTopHVG.R
@@ -62,7 +62,7 @@ plotTopHVG <- function(inSCE,
     hvgNumber <- length(hvgList)
   } else if (!is.null(hvgNumber)) {
     hvgList <- getTopHVG(inSCE = inSCE, method = method, hvgNumber = hvgNumber,
-                         featureDisplay = NULL)
+                         featureDisplay = NULL, useFeatureSubset = NULL)
   }
   if (is.null(hvgNumber) || hvgNumber == 0) {
     redIdx <- logical()

diff --git a/tests/testthat/test-featureSelection.R b/tests/testthat/test-featureSelection.R
@@ -26,21 +26,21 @@ test_that(desc = "Testing FindHVG", {
     sce <- setTopHVG(sce, "modelGeneVar", hvgNumber = 2000, altExp = TRUE, featureSubsetName = NULL)
     nHVG <- length(getTopHVG(sce, useFeatureSubset = "HVG_modelGeneVar2000"))
 
-    # testthat::expect_true(is.logical(rowData(sce)$HVG_modelGeneVar2000))
-    # testthat::expect_equal(nrow(altExp(sce, "HVG_modelGeneVar2000")), nHVG)
-    # testthat::expect_equal(metadata(sce)$sctk$featureSubsets$HVG_modelGeneVar2000$useAssay,
-    #                        "seuratNormData")
-    # 
-    # hvgs <- getTopHVG(sce, "mean.var.plot", hvgNumber = 2000,
-    #                   featureDisplay = "feature_name")
-    # testthat::expect_false(all(startsWith(hvgs, "ENSG00000")))
-    # hvgs <- getTopHVG(sce, "vst", hvgNumber = 2000)
-    # vm1 <- plotTopHVG(sce, "dispersion")
-    # vm2 <- plotTopHVG(sce, "modelGeneVar", hvgNumber = 30, labelsCount = 10,
-    #                  featureDisplay = "feature_name")
-    # vm3 <- plotTopHVG(sce, method = "mean.var.plot",
-    #                   useFeatureSubset = "HVG_modelGeneVar2000")
-    # testthat::expect_true(inherits(vm1, "ggplot"))
-    # testthat::expect_true(inherits(vm2, "ggplot"))
-    # testthat::expect_true(inherits(vm3, "ggplot"))
+    testthat::expect_true(is.logical(rowData(sce)$HVG_modelGeneVar2000))
+    testthat::expect_equal(nrow(altExp(sce, "HVG_modelGeneVar2000")), nHVG)
+    testthat::expect_equal(metadata(sce)$sctk$featureSubsets$HVG_modelGeneVar2000$useAssay,
+                           "seuratNormData")
+
+    hvgs <- getTopHVG(sce, "mean.var.plot", hvgNumber = 2000,
+                      featureDisplay = "feature_name", useFeatureSubset = NULL)
+    testthat::expect_false(all(startsWith(hvgs, "ENSG00000")))
+    hvgs <- getTopHVG(sce, "vst", hvgNumber = 2000, useFeatureSubset = NULL)
+    vm1 <- plotTopHVG(sce, "dispersion", hvgNumber = NULL)
+    vm2 <- plotTopHVG(sce, "modelGeneVar", hvgNumber = 30, labelsCount = 10,
+                     featureDisplay = "feature_name")
+    vm3 <- plotTopHVG(sce, method = "mean.var.plot",
+                      useFeatureSubset = "HVG_modelGeneVar2000", hvgNumber = NULL)
+    testthat::expect_true(inherits(vm1, "ggplot"))
+    testthat::expect_true(inherits(vm2, "ggplot"))
+    testthat::expect_true(inherits(vm3, "ggplot"))
 })