From 4f6a4fcaae707ea583ce28039c564f8899f27f30 Mon Sep 17 00:00:00 2001
From: Luke Zappia <lazappi@users.noreply.github.com>
Date: Tue, 30 Jan 2018 17:53:53 +1100
Subject: [PATCH] Add tests
---
R/BASiCSParams-methods.R | 2 +-
R/utils.R | 3 ++
tests/testthat/test-BASiCSParams.R | 15 +++++--
tests/testthat/test-Lun2Params.R | 8 +++-
tests/testthat/test-LunParams.R | 17 ++++++++
tests/testthat/test-MFAEstimate.R | 9 +++++
tests/testthat/test-MFAParams.R | 7 ++++
tests/testthat/test-PhenoParams.R | 17 +++++---
tests/testthat/test-SCDDParams.R | 21 ++++++----
tests/testthat/test-SCE-functions.R | 22 ++++++++++-
tests/testthat/test-SimpleParams.R | 7 ++++
tests/testthat/test-SplatParams.R | 31 ++++++++-------
tests/testthat/test-ZINBParams.R | 9 ++++-
tests/testthat/test-compare.R | 59 ++++++++++++++++++++++++++++
tests/testthat/test-listSims.R | 10 +++++
tests/testthat/test-lunEstimate.R | 9 +++++
tests/testthat/test-phenoEstimate.R | 9 +++++
tests/testthat/test-simpleEstimate.R | 9 +++++
tests/testthat/test-splat-simulate.R | 6 ++-
tests/testthat/test-utils.R | 22 +++++++++++
20 files changed, 252 insertions(+), 40 deletions(-)
create mode 100644 tests/testthat/test-LunParams.R
create mode 100644 tests/testthat/test-MFAEstimate.R
create mode 100644 tests/testthat/test-MFAParams.R
create mode 100644 tests/testthat/test-SimpleParams.R
create mode 100644 tests/testthat/test-compare.R
create mode 100644 tests/testthat/test-listSims.R
create mode 100644 tests/testthat/test-lunEstimate.R
create mode 100644 tests/testthat/test-phenoEstimate.R
create mode 100644 tests/testthat/test-simpleEstimate.R
create mode 100644 tests/testthat/test-utils.R
diff --git a/R/BASiCSParams-methods.R b/R/BASiCSParams-methods.R
index 90243b2..55bc5de 100644
--- a/R/BASiCSParams-methods.R
+++ b/R/BASiCSParams-methods.R
@@ -68,7 +68,7 @@ setValidity("BASiCSParams", function(object) {
})
#' @rdname setParam
-setMethod("setParam", "BASiCSParams",function(object, name, value) {
+setMethod("setParam", "BASiCSParams", function(object, name, value) {
checkmate::assertString(name)
if (name == "nCells" || name == "nBatches") {
diff --git a/R/utils.R b/R/utils.R
index 39e770d..0a90987 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -23,6 +23,9 @@ logistic <- function(x, x0, k) {
#' common columns.
rbindMatched <- function(df1, df2) {
common.names <- intersect(colnames(df1), colnames(df2))
+ if (length(common.names) < 2) {
+ stop("There must be at least two columns in common")
+ }
combined <- rbind(df1[, common.names], df2[, common.names])
return(combined)
diff --git a/tests/testthat/test-BASiCSParams.R b/tests/testthat/test-BASiCSParams.R
index 541abc1..97866e7 100644
--- a/tests/testthat/test-BASiCSParams.R
+++ b/tests/testthat/test-BASiCSParams.R
@@ -1,7 +1,12 @@
context("BASiCSParams")
+params <- newBASiCSParams()
+
+test_that("printing works", {
+ expect_output(show(params), "A Params object of class BASiCSParams")
+})
+
test_that("gene.params checks work", {
- params <- newBASiCSParams()
expect_error(setParam(params, "gene.params", data.frame(A = 1, B = 1)),
"gene.params: Incorrect column names")
expect_error(setParam(params, "gene.params",
@@ -10,7 +15,6 @@ test_that("gene.params checks work", {
})
test_that("cell.params checks work", {
- params <- newBASiCSParams()
expect_error(setParam(params, "cell.params", data.frame(A = 1, B = 1)),
"cell.params: Incorrect column names")
expect_error(setParam(params, "cell.params",
@@ -19,9 +23,14 @@ test_that("cell.params checks work", {
})
test_that("nBatches checks work", {
- params <- newBASiCSParams()
expect_error(setParam(params, "nCells", 1),
"nCells cannot be set directly, set batchCells instead")
expect_error(setParam(params, "nBatches", 1),
"nBatches cannot be set directly, set batchCells instead")
})
+
+test_that("batchCells checks work", {
+ pp <- setParam(params, "batchCells", c(10, 10))
+ expect_equal(getParam(pp, "nCells"), 20)
+ expect_equal(getParam(pp, "nBatches"), 2)
+})
diff --git a/tests/testthat/test-Lun2Params.R b/tests/testthat/test-Lun2Params.R
index 5fb6062..98d424f 100644
--- a/tests/testthat/test-Lun2Params.R
+++ b/tests/testthat/test-Lun2Params.R
@@ -1,7 +1,12 @@
context("Lun2Params")
+params <- newLun2Params()
+
+test_that("printing works", {
+ expect_output(show(params), "A Params object of class Lun2Params")
+})
+
test_that("nCells checks work", {
- params <- newLun2Params()
expect_error(setParam(params, "nCells", 1),
"nCells cannot be set directly, set cell.plates instead")
expect_error(setParam(params, "nPlates", 1),
@@ -9,7 +14,6 @@ test_that("nCells checks work", {
})
test_that("gene.params checks work", {
- params <- newLun2Params()
expect_error(setParam(params, "gene.params", data.frame(A = 1, B = 1)),
"gene.params: Incorrect column names")
expect_error(setParam(params, "gene.params",
diff --git a/tests/testthat/test-LunParams.R b/tests/testthat/test-LunParams.R
new file mode 100644
index 0000000..5f5720b
--- /dev/null
+++ b/tests/testthat/test-LunParams.R
@@ -0,0 +1,17 @@
+context("LunParams")
+
+params <- newLunParams()
+
+test_that("printing works", {
+ expect_output(show(params), "A Params object of class LunParams")
+})
+
+test_that("nCells checks work", {
+ expect_error(setParam(params, "nCells", 1),
+ "nCells cannot be set directly, set groupCells instead")
+})
+
+test_that("nGroups checks work", {
+ expect_error(setParam(params, "nGroups", 1),
+ "nGroups cannot be set directly, set groupCells instead")
+})
diff --git a/tests/testthat/test-MFAEstimate.R b/tests/testthat/test-MFAEstimate.R
new file mode 100644
index 0000000..12cee5c
--- /dev/null
+++ b/tests/testthat/test-MFAEstimate.R
@@ -0,0 +1,9 @@
+context("MFAEstimate")
+
+library(scater)
+data("sc_example_counts")
+
+test_that("MFAEstimate works", {
+ params <- mfaEstimate(sc_example_counts)
+ expect_true(validObject(params))
+})
diff --git a/tests/testthat/test-MFAParams.R b/tests/testthat/test-MFAParams.R
new file mode 100644
index 0000000..1cd9c19
--- /dev/null
+++ b/tests/testthat/test-MFAParams.R
@@ -0,0 +1,7 @@
+context("MFAParams")
+
+params <- newMFAParams()
+
+test_that("printing works", {
+ expect_output(show(params), "A Params object of class MFAParams")
+})
diff --git a/tests/testthat/test-PhenoParams.R b/tests/testthat/test-PhenoParams.R
index d5a252d..d806e99 100644
--- a/tests/testthat/test-PhenoParams.R
+++ b/tests/testthat/test-PhenoParams.R
@@ -1,15 +1,20 @@
context("PhenoParams")
+params <- newPhenoParams()
+
test_that("constructor is valid", {
- expect_true(validObject(newPhenoParams()))
+ expect_true(validObject(params))
+})
+
+test_that("printing works", {
+ expect_output(show(params), "A Params object of class PhenoParams")
})
test_that("nGenes checks work", {
- params <- newPhenoParams()
expect_error(setParam(params, "nGenes", 1),
"nGenes cannot be set directly")
- params <- setParam(params, "n.de", 0)
- total <- getParam(params, "n.de") + getParam(params, "n.pst") +
- getParam(params, "n.pst.beta") + getParam(params, "n.de.pst.beta")
- expect_equal(getParam(params, "nGenes"), total)
+ pp <- setParam(params, "n.de", 0)
+ total <- getParam(pp, "n.de") + getParam(pp, "n.pst") +
+ getParam(pp, "n.pst.beta") + getParam(pp, "n.de.pst.beta")
+ expect_equal(getParam(pp, "nGenes"), total)
})
diff --git a/tests/testthat/test-SCDDParams.R b/tests/testthat/test-SCDDParams.R
index da4d061..05ff5ef 100644
--- a/tests/testthat/test-SCDDParams.R
+++ b/tests/testthat/test-SCDDParams.R
@@ -1,17 +1,22 @@
context("SCDDParams")
+params <- newSCDDParams()
+
test_that("constructor is valid", {
- expect_true(validObject(newSCDDParams()))
+ expect_true(validObject(params))
+})
+
+test_that("printing works", {
+ expect_output(show(params), "A Params object of class SCDDParams")
})
test_that("nGenes checks work", {
- params <- newSCDDParams()
expect_error(setParam(params, "nGenes", 1),
paste("nGenes cannot be set directly, set nDE, nDP, nDM, nDB,",
"nEE or nEP instead"))
- params <- setParam(params, "nEE", 0)
- total <- getParam(params, "nDE") + getParam(params, "nDP") +
- getParam(params, "nDM") + getParam(params, "nDP") +
- getParam(params, "nEE") + getParam(params, "nEP")
- expect_equal(getParam(params, "nGenes"), total)
-})
\ No newline at end of file
+ pp <- setParam(params, "nEE", 0)
+ total <- getParam(pp, "nDE") + getParam(pp, "nDP") +
+ getParam(pp, "nDM") + getParam(pp, "nDP") +
+ getParam(pp, "nEE") + getParam(pp, "nEP")
+ expect_equal(getParam(pp, "nGenes"), total)
+})
diff --git a/tests/testthat/test-SCE-functions.R b/tests/testthat/test-SCE-functions.R
index 83e002d..973cf54 100644
--- a/tests/testthat/test-SCE-functions.R
+++ b/tests/testthat/test-SCE-functions.R
@@ -1,7 +1,26 @@
context("SCE functions")
+sce <- simpleSimulate()
+
+test_that("addFeatureStats works with counts", {
+ ss <- addFeatureStats(sce)
+ expect_true(all(c("MeanCounts", "VarCounts", "CVCounts", "MedCounts",
+ "MADCounts") %in% colnames(rowData(ss))))
+ ss <- addFeatureStats(sce, log = TRUE)
+ expect_true(all(c("MeanLogCounts", "VarLogCounts", "CVLogCounts",
+ "MedLogCounts", "MADLogCounts") %in%
+ colnames(rowData(ss))))
+ ss <- addFeatureStats(sce, no.zeros = TRUE)
+ expect_true(all(c("MeanCountsNo0", "VarCountsNo0", "CVCountsNo0",
+ "MedCountsNo0", "MADCountsNo0") %in%
+ colnames(rowData(ss))))
+ ss <- addFeatureStats(sce, log = TRUE, no.zeros = TRUE)
+ expect_true(all(c("MeanLogCountsNo0", "VarLogCountsNo0", "CVLogCountsNo0",
+ "MedLogCountsNo0", "MADLogCountsNo0") %in%
+ colnames(rowData(ss))))
+})
+
test_that("addGeneLengths generate method works", {
- sce <- simpleSimulate()
expect_silent(addGeneLengths(sce))
expect_error(addGeneLengths("a"))
expect_error(addGeneLengths(sce, loc = "a"))
@@ -10,7 +29,6 @@ test_that("addGeneLengths generate method works", {
})
test_that("addGeneLength sample method works", {
- sce <- simpleSimulate()
lens <- round(runif(100, 100, 10000))
expect_silent(addGeneLengths(sce, method = "sample", lengths = lens))
expect_error(addGeneLengths(sce, method = "sample"))
diff --git a/tests/testthat/test-SimpleParams.R b/tests/testthat/test-SimpleParams.R
new file mode 100644
index 0000000..3fa78dc
--- /dev/null
+++ b/tests/testthat/test-SimpleParams.R
@@ -0,0 +1,7 @@
+context("SimpleParams")
+
+params <- newSimpleParams()
+
+test_that("printing works", {
+ expect_output(show(params), "A Params object of class SimpleParams")
+})
diff --git a/tests/testthat/test-SplatParams.R b/tests/testthat/test-SplatParams.R
index 208f0df..91695df 100644
--- a/tests/testthat/test-SplatParams.R
+++ b/tests/testthat/test-SplatParams.R
@@ -1,7 +1,12 @@
context("SplatParams")
+params <- newSplatParams()
+
+test_that("printing works", {
+ expect_output(show(params), "A Params object of class SplatParams")
+})
+
test_that("nBatches checks work", {
- params <- newSplatParams()
expect_error(setParam(params, "nCells", 1),
"nCells cannot be set directly, set batchCells instead")
expect_error(setParam(params, "nBatches", 1),
@@ -9,22 +14,20 @@ test_that("nBatches checks work", {
})
test_that("nGroups checks work", {
- params <- newSplatParams()
expect_error(setParam(params, "nGroups", 1),
"nGroups cannot be set directly, set group.prob instead")
})
test_that("path.from checks work", {
- params <- newSplatParams()
- params <- setParams(params, group.prob = c(0.5, 0.5))
- params <- setParamUnchecked(params, "path.from", c(0, 1))
- expect_silent(validObject(params))
- params <- setParamUnchecked(params, "path.from", c(0, 3))
- expect_error(validObject(params), "invalid class")
- params <- setParamUnchecked(params, "path.from", c(1, 0))
- expect_error(validObject(params), "path cannot begin at itself")
- params <- newSplatParams()
- params <- setParams(params, group.prob = c(0.3, 0.3, 0.4))
- params <- setParamUnchecked(params, "path.from", c(2, 1, 1))
- expect_error(validObject(params), "origin must be specified in path.from")
+ pp <- setParams(params, group.prob = c(0.5, 0.5))
+ pp <- setParamUnchecked(pp, "path.from", c(0, 1))
+ expect_silent(validObject(pp))
+ pp <- setParamUnchecked(pp, "path.from", c(0, 3))
+ expect_error(validObject(pp), "invalid class")
+ pp <- setParamUnchecked(pp, "path.from", c(1, 0))
+ expect_error(validObject(pp), "path cannot begin at itself")
+ pp <- newSplatParams()
+ pp <- setParams(pp, group.prob = c(0.3, 0.3, 0.4))
+ pp <- setParamUnchecked(pp, "path.from", c(2, 1, 1))
+ expect_error(validObject(pp), "origin must be specified in path.from")
})
diff --git a/tests/testthat/test-ZINBParams.R b/tests/testthat/test-ZINBParams.R
index bbb7abd..061bb8a 100644
--- a/tests/testthat/test-ZINBParams.R
+++ b/tests/testthat/test-ZINBParams.R
@@ -1,11 +1,16 @@
context("ZINBParams")
+params <- newZINBParams()
+
test_that("constructor is valid", {
- expect_true(validObject(newZINBParams()))
+ expect_true(validObject(params))
+})
+
+test_that("printing works", {
+ expect_output(show(params), "A Params object of class ZINBParams")
})
test_that("nGenes checks work", {
- params <- newZINBParams()
expect_error(setParam(params, "nGenes", 1),
"nGenes cannot be set directly")
expect_error(setParam(params, "nCells", 1),
diff --git a/tests/testthat/test-compare.R b/tests/testthat/test-compare.R
new file mode 100644
index 0000000..04d6520
--- /dev/null
+++ b/tests/testthat/test-compare.R
@@ -0,0 +1,59 @@
+context("Comparison functions")
+
+sim1 <- splatSimulate(nGenes = 1000, batchCells = 20)
+sim2 <- simpleSimulate(nGenes = 1000, nCells = 20)
+
+comparison <- compareSCEs(list(Splat = sim1, Simple = sim2))
+difference <- diffSCEs(list(Splat = sim1, Simple = sim2), ref = "Simple")
+
+test_that("compareSCEs works", {
+ expect_length(comparison, 3)
+ expect_true(all(c("FeatureData", "PhenoData", "Plots") %in%
+ names(comparison)))
+ checkmate::expect_class(comparison$PhenoData, "data.frame")
+ checkmate::expect_class(comparison$FeatureData, "data.frame")
+ expect_length(comparison$Plots, 7)
+ expect_true(all(c("Means", "Variances", "MeanVar", "LibrarySizes",
+ "ZerosGene", "ZerosCell", "MeanZeros") %in%
+ names(comparison$Plots)))
+ for (plot in names(comparison$Plots)) {
+ checkmate::expect_class(comparison$Plots[[plot]], "ggplot")
+ }
+})
+
+test_that("diffSCEs works", {
+ expect_length(difference, 5)
+ expect_true(all(c("Reference", "FeatureData", "PhenoData", "Plots",
+ "QQPlots") %in% names(difference)))
+ checkmate::expect_class(difference$Reference, "SingleCellExperiment")
+ checkmate::expect_class(difference$PhenoData, "data.frame")
+ checkmate::expect_class(difference$FeatureData, "data.frame")
+ expect_length(difference$Plots, 7)
+ expect_true(all(c("Means", "Variances", "MeanVar", "LibrarySizes",
+ "ZerosGene", "ZerosCell", "MeanZeros") %in%
+ names(difference$Plots)))
+ for (plot in names(difference$Plots)) {
+ checkmate::expect_class(difference$Plots[[plot]], "ggplot")
+ }
+ expect_length(difference$QQPlots, 5)
+ expect_true(all(c("Means", "Variances", "LibrarySizes", "ZerosGene",
+ "ZerosCell") %in% names(difference$QQPlots)))
+ for (plot in names(difference$QQPlots)) {
+ checkmate::expect_class(difference$QQPlots[[plot]], "ggplot")
+ }
+})
+
+# test_that("makeCompPanel works", {
+# panel <- makeCompPanel(comparison)
+# checkmate::expect_class(panel, "ggplot")
+# })
+#
+# test_that("makeDiffPanel works", {
+# panel <- makeDiffPanel(difference)
+# checkmate::expect_class(panel, "ggplot")
+# })
+#
+# test_that("makeOverallPanel works", {
+# panel <- makeOverallPanel(comparison, difference)
+# checkmate::expect_class(panel, "ggplot")
+# })
diff --git a/tests/testthat/test-listSims.R b/tests/testthat/test-listSims.R
new file mode 100644
index 0000000..cf386c9
--- /dev/null
+++ b/tests/testthat/test-listSims.R
@@ -0,0 +1,10 @@
+context("listSims")
+
+test_that("listSims printing works", {
+ expect_output(listSims(), "Splatter currently contains")
+})
+
+test_that("listSims return works", {
+ ll <- listSims(print = FALSE)
+ checkmate::expect_class(ll, "data.frame")
+})
diff --git a/tests/testthat/test-lunEstimate.R b/tests/testthat/test-lunEstimate.R
new file mode 100644
index 0000000..010ae35
--- /dev/null
+++ b/tests/testthat/test-lunEstimate.R
@@ -0,0 +1,9 @@
+context("lunEstimate")
+
+library(scater)
+data("sc_example_counts")
+
+test_that("lunEstimate works", {
+ params <- lunEstimate(sc_example_counts)
+ expect_true(validObject(params))
+})
diff --git a/tests/testthat/test-phenoEstimate.R b/tests/testthat/test-phenoEstimate.R
new file mode 100644
index 0000000..402d781
--- /dev/null
+++ b/tests/testthat/test-phenoEstimate.R
@@ -0,0 +1,9 @@
+context("phenoEstimate")
+
+library(scater)
+data("sc_example_counts")
+
+test_that("phenoEstimate works", {
+ params <- phenoEstimate(sc_example_counts)
+ expect_true(validObject(params))
+})
diff --git a/tests/testthat/test-simpleEstimate.R b/tests/testthat/test-simpleEstimate.R
new file mode 100644
index 0000000..3b581e1
--- /dev/null
+++ b/tests/testthat/test-simpleEstimate.R
@@ -0,0 +1,9 @@
+context("simpleEstimate")
+
+library(scater)
+data("sc_example_counts")
+
+test_that("simpleEstimate works", {
+ params <- simpleEstimate(sc_example_counts)
+ expect_true(validObject(params))
+})
diff --git a/tests/testthat/test-splat-simulate.R b/tests/testthat/test-splat-simulate.R
index 9d99cf7..d5b16f5 100644
--- a/tests/testthat/test-splat-simulate.R
+++ b/tests/testthat/test-splat-simulate.R
@@ -4,9 +4,11 @@ test.params <- newSplatParams(nGenes = 100, batchCells = c(5, 5),
group.prob = c(0.5, 0.5), lib.scale = 0)
test_that("splatSimulate output is valid", {
- expect_true(validObject(splatSimulate(test.params, method = "single")))
+ expect_true(validObject(splatSimulate(test.params, method = "single",
+ dropout.present = TRUE)))
expect_true(validObject(splatSimulate(test.params, method = "groups")))
- expect_true(validObject(splatSimulate(test.params, method = "paths")))
+ expect_true(validObject(splatSimulate(test.params, method = "paths",
+ path.from = c(0, 1))))
})
test_that("one group switches to single mode", {
diff --git a/tests/testthat/test-utils.R b/tests/testthat/test-utils.R
new file mode 100644
index 0000000..d4b7bdc
--- /dev/null
+++ b/tests/testthat/test-utils.R
@@ -0,0 +1,22 @@
+context("utils")
+
+test_that("logistic function works", {
+ expect_equal(logistic(0, x0 = 0, k = 1), 0.5)
+})
+
+test_that("rbindMatched works", {
+ df1 <- data.frame(A = 1:3, B = 4:6, C = 7:9)
+ df2 <- data.frame(D = 0)
+ expect_error(rbindMatched(df1, df2),
+ "There must be at least two columns in common")
+ df2 <- data.frame(A = 1:3)
+ expect_error(rbindMatched(df1, df2),
+ "There must be at least two columns in common")
+ df2 <- data.frame(A = 1:3, C = 7:9, D = 0)
+ expect_equal(colnames(rbindMatched(df1, df2)), c("A", "C"))
+})
+
+test_that("winsorize works", {
+ x <- c(0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2)
+ expect_true(all(winsorize(x, q = 0.1) == 1))
+})
--
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