amended subsample() as to keep the original order of events

- amended subsample()
- updated unit tests accordingly
- reactivated all unit tests related to ggplot category

R/utils.R

@@ -124,6 +124,9 @@ subsample <- function(ff, nEvents, seed = NULL, ...) {
             replace = FALSE
         )
     }
+
+    # order the kept events to maintain chronology of events ! 
+    keep <- sort(keep)
 
     # add Original_ID as a new column if necessary
     ff <- appendCellID(ff)

tests/testthat/test-CytoProcessingStepImplementations.R

@@ -97,36 +97,6 @@ test_that("estimateScaleTransforms work", {
     )
 })
 
-# test_that("selectRandomSamples works", {
-#     rawDataDir <-
-#         system.file("extdata", package = "CytoPipeline")
-#     sampleFiles <-
-#         file.path(rawDataDir, list.files(rawDataDir, pattern = "Donor"))
-#     
-#     seed <- 2
-#     nSamples <- 1
-#     
-#     newSampleFiles <- selectRandomSamples(sampleFiles, 
-#                                           nSamples = nSamples,
-#                                           seed = seed)
-#     expected <- sampleFiles[1]
-#     expect_equal(newSampleFiles,
-#                  expected)
-#     
-#     newSampleFiles <- selectRandomSamples(sampleFiles, 
-#                                           nSamples = 3,
-#                                           seed = seed)
-#     
-#     expect_equal(newSampleFiles,
-#                  sampleFiles)
-#     
-#     expect_error(selectRandomSamples(sampleFiles, 
-#                                      nSamples = 0,
-#                                      seed = seed),
-#                  regexp = "should be a numeric >= 1")
-#                                           
-#         
-# })
 
 test_that("readSampleFiles with no sample files gives an error", {
     rawDataDir <-
@@ -551,7 +521,7 @@ test_that("removeDebrisManualGate works", {
 
     ref_ff_cells <- readRDS(test_path("fixtures", "ff_cells_manual_gate.rds"))
 
-    #saveRDS(ff_cells, test_path("fixtures", "ff_cells_manual_gate.rds"))
+    # saveRDS(ff_cells, test_path("fixtures", "ff_cells_manual_gate.rds"))
 
     expect_equal(
         flowCore::exprs(ff_cells),
@@ -575,7 +545,7 @@ test_that("removeDeadCellsManualGate works", {
 
     ref_ff_lcells <- readRDS(test_path("fixtures", "ff_lcells_manual_gate.rds"))
 
-    #saveRDS(ff_lcells, test_path("fixtures", "ff_lcells_manual_gate.rds"))
+    # saveRDS(ff_lcells, test_path("fixtures", "ff_lcells_manual_gate.rds"))
 
     expect_equal(
         flowCore::exprs(ff_lcells),

tests/testthat/test-gating.R

@@ -21,117 +21,106 @@ path <- system.file("scripts",
 
 source(file.path(path,"MakeOMIP021UTSamples.R"))
 
-# TO DO: reactivate tests when ggplot version is fixed
-# error message (issue with vdiffr::expect_doppelganger())
-# Backtrace:
-# 1. └─vdiffr::expect_doppelganger(...) at test-ggplots.R:58:4
-# 2.   └─vdiffr (local) writer(fig, testcase, title)
-# 3.     └─vdiffr:::svglite(file)
-# 4.       └─vdiffr:::svglite_(...)
-# ── Error ('test-ggplots.R:175'): ggplotEvents with 2D works ────────────────────
-# Error in `svglite_(filename, bg, width, height, pointsize, standalone, 
-#                    always_valid)`: Graphics API version mismatch
-
-# test_that("singletsGate works", {
-#     mySingletsGate <- singletsGate(OMIP021UTSamples[[1]])
-# 
-#     selectedSinglets <- flowCore::filter(
-#         OMIP021UTSamples[[1]],
-#         mySingletsGate
-#     )
-#     ff_l <- flowCore::Subset(OMIP021UTSamples[[1]], selectedSinglets)
-# 
-#     linRange <- c(0, 250000)
-#     p <- ggplotFilterEvents(
-#         ffPre = OMIP021UTSamples[[1]],
-#         ffPost = ff_l,
-#         seed = 1,
-#         xChannel = "FSC-A", xLinearRange = linRange,
-#         yChannel = "FSC-H", yLinearRange = linRange
-#     )
-# 
-#     vdiffr::expect_doppelganger("singletsGate default channels", fig = p)
-# 
-#     mySingletsGate <- singletsGate(OMIP021UTSamples[[1]], nmad = 3)
-# 
-#     selectedSinglets <- flowCore::filter(
-#         OMIP021UTSamples[[1]],
-#         mySingletsGate
-#     )
-#     ff_l <- flowCore::Subset(OMIP021UTSamples[[1]], selectedSinglets)
-# 
-#     p <- ggplotFilterEvents(
-#         ffPre = OMIP021UTSamples[[1]],
-#         ffPost = ff_l,
-#         seed = 1,
-#         xChannel = "FSC-A", xLinearRange = linRange,
-#         yChannel = "FSC-H", yLinearRange = linRange
-#     )
-# 
-#     vdiffr::expect_doppelganger(
-#         "singletsGate default channels with fixed nmad",
-#         fig = p
-#     )
-# 
-#     mySingletsGate <- singletsGate(OMIP021UTSamples[[1]],
-#         channel1 = "SSC-A",
-#         channel2 = "SSC-H"
-#     )
-# 
-#     selectedSinglets <- flowCore::filter(
-#         OMIP021UTSamples[[1]],
-#         mySingletsGate
-#     )
-#     ff_l <- flowCore::Subset(OMIP021UTSamples[[1]], selectedSinglets)
-# 
-#     p <- ggplotFilterEvents(
-#         ffPre = OMIP021UTSamples[[1]],
-#         ffPost = ff_l,
-#         seed = 1,
-#         xChannel = "SSC-A", xLinearRange = linRange,
-#         yChannel = "SSC-H", yLinearRange = linRange
-#     )
-# 
-#     vdiffr::expect_doppelganger("singletsGate selected channels", fig = p)
-# 
-#     # test application of two gates one after the other
-#     singletsGate1 <- singletsGate(OMIP021UTSamples[[1]], nmad = 3)
-#     singletsGate2 <- singletsGate(OMIP021UTSamples[[1]],
-#         channel1 = "SSC-A",
-#         channel2 = "SSC-H",
-#         filterId = "Singlets2"
-#     )
-# 
-#     singletCombinedGate <- singletsGate1 & singletsGate2
-# 
-#     selectedSinglets <- flowCore::filter(
-#         OMIP021UTSamples[[1]],
-#         singletCombinedGate
-#     )
-# 
-#     ff_l <- flowCore::Subset(OMIP021UTSamples[[1]], selectedSinglets)
-# 
-#     p1 <- ggplotFilterEvents(
-#         ffPre = OMIP021UTSamples[[1]],
-#         ffPost = ff_l,
-#         seed = 1,
-#         xChannel = "FSC-A", xLinearRange = linRange,
-#         yChannel = "FSC-H", yLinearRange = linRange
-#     )
-# 
-#     p2 <- ggplotFilterEvents(
-#         ffPre = OMIP021UTSamples[[1]],
-#         ffPost = ff_l,
-#         seed = 1,
-#         xChannel = "SSC-A", xLinearRange = linRange,
-#         yChannel = "SSC-H", yLinearRange = linRange
-#     )
-# 
-# 
-#     vdiffr::expect_doppelganger("singletsGates one after the other - fig1",
-#         fig = p1
-#     )
-#     vdiffr::expect_doppelganger("singletsGates one after the other - fig2",
-#         fig = p2
-#     )
-# })
+test_that("singletsGate works", {
+    mySingletsGate <- singletsGate(OMIP021UTSamples[[1]])
+
+    selectedSinglets <- flowCore::filter(
+        OMIP021UTSamples[[1]],
+        mySingletsGate
+    )
+    ff_l <- flowCore::Subset(OMIP021UTSamples[[1]], selectedSinglets)
+
+    linRange <- c(0, 250000)
+    p <- ggplotFilterEvents(
+        ffPre = OMIP021UTSamples[[1]],
+        ffPost = ff_l,
+        seed = 1,
+        xChannel = "FSC-A", xLinearRange = linRange,
+        yChannel = "FSC-H", yLinearRange = linRange
+    )
+
+    vdiffr::expect_doppelganger("singletsGate default channels", fig = p)
+
+    mySingletsGate <- singletsGate(OMIP021UTSamples[[1]], nmad = 3)
+
+    selectedSinglets <- flowCore::filter(
+        OMIP021UTSamples[[1]],
+        mySingletsGate
+    )
+    ff_l <- flowCore::Subset(OMIP021UTSamples[[1]], selectedSinglets)
+
+    p <- ggplotFilterEvents(
+        ffPre = OMIP021UTSamples[[1]],
+        ffPost = ff_l,
+        seed = 1,
+        xChannel = "FSC-A", xLinearRange = linRange,
+        yChannel = "FSC-H", yLinearRange = linRange
+    )
+
+    vdiffr::expect_doppelganger(
+        "singletsGate default channels with fixed nmad",
+        fig = p
+    )
+
+    mySingletsGate <- singletsGate(OMIP021UTSamples[[1]],
+        channel1 = "SSC-A",
+        channel2 = "SSC-H"
+    )
+
+    selectedSinglets <- flowCore::filter(
+        OMIP021UTSamples[[1]],
+        mySingletsGate
+    )
+    ff_l <- flowCore::Subset(OMIP021UTSamples[[1]], selectedSinglets)
+
+    p <- ggplotFilterEvents(
+        ffPre = OMIP021UTSamples[[1]],
+        ffPost = ff_l,
+        seed = 1,
+        xChannel = "SSC-A", xLinearRange = linRange,
+        yChannel = "SSC-H", yLinearRange = linRange
+    )
+
+    vdiffr::expect_doppelganger("singletsGate selected channels", fig = p)
+
+    # test application of two gates one after the other
+    singletsGate1 <- singletsGate(OMIP021UTSamples[[1]], nmad = 3)
+    singletsGate2 <- singletsGate(OMIP021UTSamples[[1]],
+        channel1 = "SSC-A",
+        channel2 = "SSC-H",
+        filterId = "Singlets2"
+    )
+
+    singletCombinedGate <- singletsGate1 & singletsGate2
+
+    selectedSinglets <- flowCore::filter(
+        OMIP021UTSamples[[1]],
+        singletCombinedGate
+    )
+
+    ff_l <- flowCore::Subset(OMIP021UTSamples[[1]], selectedSinglets)
+
+    p1 <- ggplotFilterEvents(
+        ffPre = OMIP021UTSamples[[1]],
+        ffPost = ff_l,
+        seed = 1,
+        xChannel = "FSC-A", xLinearRange = linRange,
+        yChannel = "FSC-H", yLinearRange = linRange
+    )
+
+    p2 <- ggplotFilterEvents(
+        ffPre = OMIP021UTSamples[[1]],
+        ffPost = ff_l,
+        seed = 1,
+        xChannel = "SSC-A", xLinearRange = linRange,
+        yChannel = "SSC-H", yLinearRange = linRange
+    )
+
+
+    vdiffr::expect_doppelganger("singletsGates one after the other - fig1",
+        fig = p1
+    )
+    vdiffr::expect_doppelganger("singletsGates one after the other - fig2",
+        fig = p2
+    )
+})

tests/testthat/test-utils.R

@@ -13,6 +13,7 @@
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 # GNU General Public License for more details (<http://www.gnu.org/licenses/>).
 
+data("OMIP021Samples")
 
 test_that("areSignalCols works", {
     ff <- OMIP021Samples[[1]]