Added tests for new function and updating news

NEWS.md

@@ -3,6 +3,8 @@
 ## CTexploreR 1.1.3
 
 - Add pkgdown config.
+- Correcting typo in fetal_germcells_mean_methylation() function name
+- Adding tests for new functions
 
 
 ## CTexploreR 1.1.2

tests/testthat/test_embryo_expression.R

@@ -0,0 +1,32 @@
+test_that("embryo_expression() works", {
+
+  ## returns a SingleCellExperiment
+  ## n valid genes in input returns a SingleCellExperiment of n expected rownames
+  ## returns a warning when an invalid gene is entered
+  ## works with only one gene in input
+  ## error if no dataset is specified
+  expect_error(embryo_expression("MAGEA1"))
+  expect_warning(res <- embryo_expression(c("MAGEA1", "xxx"),
+                                          dataset = "Petropoulos",
+                                          values_only = TRUE), "names invalid")
+  expect_s4_class(res, "SingleCellExperiment")  
+  expect_equal(nrow(res), 1) 
+  expect_identical(rownames(res), "MAGEA1")
+
+
+  ## Test that the function returns a heatmap by default
+  ## Test that returns the expected heatmap
+  ## res <- embryo_expression(c("MAGEA1", "MAGEA3", "MAGEA4"),
+  ##                         dataset = "Petropoulos")
+  ## expect_s4_class(res, "Heatmap")
+
+  ## Same with Zhu
+  expect_warning(res <- embryo_expression(c("MAGEA1", "xxx"),
+                                          dataset = "Zhu",
+                                          values_only = TRUE), "names invalid")
+  expect_s4_class(res, "SingleCellExperiment")  
+  expect_equal(nrow(res), 1) 
+  expect_identical(rownames(res), "MAGEA1")
+
+})
+

tests/testthat/test_embryos_mean_methylation.R

@@ -0,0 +1,26 @@
+test_that("embryos_mean_methylation() works", {
+
+  ## returns a RangedSummarizedExperiment when values_only is set to TRUE
+  res <- embryos_mean_methylation(
+    genes = c("MAGEA1", "MAGEA2", "MAGEA4"), 
+    values_only = TRUE)
+  expect_s4_class(res, "RangedSummarizedExperiment")  
+  expect_equal(nrow(res), 3)
+
+  ## selects the expected cell types
+  my_stages <- c("Morula", "Blastocyst")
+  res <- embryos_mean_methylation(stage = my_stages, genes = "MAGEA1",
+                                  values_only = TRUE)
+  expect_equal(nrow(res), 1) 
+  expect_true(all(unique(colData(res)$Stage) %in% my_stages))
+
+  ## no valid gene in input returns an empty matrix
+  expect_warning(res_no_gene <- embryos_mean_methylation(
+    genes = "xxx", values_only = TRUE), "valid types")
+  expect_equal(nrow(res_no_gene), 0)
+
+  ## Test that the function returns a heatmap by default
+  ## res <- embryos_mean_methylation(
+  ##  genes = c("MAGEA1", "MAGEA2", "MAGEA4", "TDRD1"))
+  ## expect_s4_class(res, "Heatmap")
+})

tests/testthat/test_fetal_germcells_expression.R

@@ -0,0 +1,20 @@
+test_that("fetal_germcells_expression() works", {
+
+  ## returns a SingleCellExperiment
+  ## n valid genes in input returns a SingleCellExperiment of n expected rownames
+  ## returns a warning when an invalid gene is entered
+  ## works with only one gene in input
+
+  expect_warning(res <- fetal_germcells_expression(c("MAGEA1", "xxx"),
+                                          values_only = TRUE), "names invalid")
+  expect_s4_class(res, "SingleCellExperiment")  
+  expect_equal(nrow(res), 1) 
+  expect_identical(rownames(res), "MAGEA1")
+
+
+  ## Test that the function returns a heatmap by default
+  ## Test that returns the expected heatmap
+  ## res <- fetal_germcells_expression(c("MAGEA1", "MAGEA3", "MAGEA4"))
+  ## expect_s4_class(res, "Heatmap")
+
+})

tests/testthat/test_fetal_germcells_mean_methylation.R

@@ -0,0 +1,20 @@
+test_that("fetal_germcells_mean_methylation() works", {
+
+  ## returns a SummarizedExperiment when values_only is set to TRUE
+  res <- fetal_germcells_mean_methylation(
+    genes = c("MAGEA1", "MAGEA2", "MAGEA4"), 
+    values_only = TRUE)
+  expect_s4_class(res, "SummarizedExperiment")  
+  expect_equal(nrow(res), 3)
+
+
+  ## no valid gene in input returns an empty matrix
+  expect_warning(res_no_gene <- fetal_germcells_mean_methylation(
+    genes = "xxx", values_only = TRUE), "valid types")
+  expect_equal(nrow(res_no_gene), 0)
+
+  ## Test that the function returns a heatmap by default
+  ## res <- fetal_germcells_mean_methylation(
+  ##  genes = c("MAGEA1", "MAGEA2", "MAGEA4", "TDRD1"))
+  ## expect_s4_class(res, "Heatmap")
+})

tests/testthat/test_hESC_expression.R

@@ -0,0 +1,24 @@
+test_that("hESC_expression() works", {
+
+  ## returns a SummarizedExperiment
+  res <- hESC_expression(genes = c("MAGEA1", "MAGEA3"), 
+                           values_only = TRUE)
+  expect_s4_class(res, "SummarizedExperiment")
+  expect_equal(nrow(res), 2) 
+  expect_identical(sort(rowData(res)$external_gene_name), 
+                   sort(c("MAGEA1", "MAGEA3")))
+
+  ## Test the "log_TPM" units argument
+  res_in_log <- hESC_expression(c("MAGEA1", "MAGEA3"), 
+                                units = "log_TPM", 
+                                values_only = TRUE)
+  expect_equal(assay(res_in_log)[, "H1"], log1p(assay(res)[, "H1"])) 
+
+  # Check default genes with CTP
+  res_includeCTP <- hESC_expression(include_CTP = TRUE, values_only = TRUE)
+  expect_equal(nrow(res_includeCTP), nrow(CT_genes))
+
+  ## Test that the function returns a heatmap
+  ## res <- hESC_expression(genes = c("MAGEA1", "MAGEA3"))
+  ## expect_s4_class(res, "Heatmap")
+})

tests/testthat/test_hESC_mean_methylation.R

@@ -0,0 +1,27 @@
+test_that("hESC_mean_methylation() works", {
+
+  ## returns a SummarizedExperiment when values_only is set to TRUE
+  ## the na.omit parameter set to FALSE keeps genes with missing values
+  res <- hESC_mean_methylation(
+    genes = c("MAGEA1", "MAGEA2", "MAGEA4"), 
+    na.omit = FALSE, values_only = TRUE)
+  expect_s4_class(res, "SummarizedExperiment")
+  expect_equal(nrow(res), 3)
+
+  ## the na.omit parameter set to TRUE removes genes with missing values
+  res_na_omit <- hESC_mean_methylation(
+    genes = c("MAGEA1", "MAGEA2", "MAGEA4"), 
+    na.omit = TRUE, values_only = TRUE)
+  expect_identical(na.omit(res), res_na_omit)
+
+  ## no valid gene in input returns an empty matrix
+  expect_warning(res_no_gene <- hESC_mean_methylation(
+    genes = "xxx", values_only = TRUE), "valid types")
+  expect_equal(nrow(res_no_gene), 0)
+
+  ## Test that the function returns a heatmap by default
+  ## res <- hESC_mean_methylation(
+  ##  genes = c("MAGEA1", "MAGEA2", "MAGEA4", "TDRD1"))
+  ## expect_s4_class(res, "Heatmap")
+
+})

tests/testthat/test_oocytes_expression.R

@@ -0,0 +1,20 @@
+test_that("oocytes_expression() works", {
+
+  ## returns a SingleCellExperiment
+  ## n valid genes in input returns a SingleCellExperiment of n expected rownames
+  ## returns a warning when an invalid gene is entered
+  ## works with only one gene in input
+
+  expect_warning(res <- oocytes_expression(c("MAGEA1", "xxx"),
+                                                   values_only = TRUE), "names invalid")
+  expect_s4_class(res, "SingleCellExperiment")  
+  expect_equal(nrow(res), 1) 
+  expect_identical(rownames(res), "MAGEA1")
+
+
+  ## Test that the function returns a heatmap by default
+  ## Test that returns the expected heatmap
+  ## res <- oocytes_expression(c("MAGEA1", "MAGEA3", "MAGEA4"))
+  ## expect_s4_class(res, "Heatmap")
+
+})