SetDatExpr unit tests (76da474c) · Commits · github_fork / HdWGCNA

tests/testthat/test-Metacells.R

+40 −11

Original line number	Diff line number	Diff line
		@@ -12,11 +12,11 @@ test_that("Metacell output is Seurat format", {

		test_seurat <- MetacellsByGroups(
		test_seurat,
		group.by = c('Sample'),
		group.by = c('cell_type'),
		k = 5,
		max_shared = 5,
		ident.group = 'Sample',
		target_metacells=10,
		ident.group = 'cell_type',
		target_metacells=50,
		min_cells=10
		)

		@@ -39,11 +39,11 @@ test_that("Metacell features are same as Seurat object",{

		test_seurat <- MetacellsByGroups(
		test_seurat,
		group.by = c('Sample'),
		group.by = c('cell_type'),
		k = 5,
		max_shared = 5,
		ident.group = 'Sample',
		target_metacells=10,
		ident.group = 'cell_type',
		target_metacells=50,
		min_cells=10
		)

		@@ -67,17 +67,17 @@ test_that("Meta-data gets passed to the metacell object",{

		test_seurat <- MetacellsByGroups(
		test_seurat,
		group.by = c('Sample', 'cell_type', 'annotation'),
		group.by = c('cell_type', 'annotation'),
		k = 5,
		max_shared = 5,
		ident.group = 'Sample',
		target_metacells=10,
		ident.group = 'cell_type',
		target_metacells=50,
		min_cells=10
		)

		m_obj <- GetMetacellObject(test_seurat)

		expect_equal(all(c('Sample', 'cell_type', 'annotation') %in% colnames(m_obj@meta.data)), TRUE)
		expect_equal(all(c('cell_type', 'annotation') %in% colnames(m_obj@meta.data)), TRUE)

		})

		@@ -107,3 +107,32 @@ test_that("Metacell object Idents are expected", {
		expect_equal(check, TRUE)

		})

		# test that normalizing the metacells works as intended
		test_that("Normalizing the metacell object works",{
		data(test_seurat)

		test_seurat <- SetupForWGCNA(
		test_seurat,
		wgcna_name = 'test',
		features = rownames(test_seurat)
		)

		test_seurat <- MetacellsByGroups(
		test_seurat,
		group.by = c('cell_type'),
		k = 5,
		max_shared = 5,
		ident.group = 'cell_type',
		target_metacells=50,
		min_cells=10
		)

		test_seurat <- NormalizeMetacells(test_seurat, verbose=FALSE)
		m_obj <- GetMetacellObject(test_seurat)
		expr <- Seurat::GetAssayData(test_seurat, slot='data')

		check <- all.equal(ceiling(expr), expr) == TRUE
		expect_equal(check, FALSE)

		})

tests/testthat/test-SetDatExpr.R

0 → 100644

+153 −0

Original line number	Diff line number	Diff line
		# test that the output format is expected
		test_that("SetDatExpr output is a data.frame", {

		data(test_seurat)

		test_seurat <- SetupForWGCNA(
		test_seurat,
		wgcna_name = 'test',
		features = rownames(test_seurat)
		)

		test_seurat <- MetacellsByGroups(
		test_seurat,
		group.by = c('cell_type'),
		k = 5,
		max_shared = 5,
		ident.group = 'cell_type',
		target_metacells=50,
		min_cells=10
		)
		test_seurat <- NormalizeMetacells(test_seurat, verbose=FALSE)
		test_seurat <- SetDatExpr(test_seurat, assay = 'RNA')
		datExpr <- GetDatExpr(test_seurat)
		expect_equal(class(datExpr), "data.frame")

		})

		# check that the datExpr has features for columns
		test_that("features are columns", {

		data(test_seurat)

		test_seurat <- SetupForWGCNA(
		test_seurat,
		wgcna_name = 'test',
		features = rownames(test_seurat)
		)

		test_seurat <- MetacellsByGroups(
		test_seurat,
		group.by = c('cell_type'),
		k = 5,
		max_shared = 5,
		ident.group = 'cell_type',
		target_metacells=50,
		min_cells=10
		)
		test_seurat <- NormalizeMetacells(test_seurat, verbose=FALSE)
		test_seurat <- SetDatExpr(test_seurat, assay = 'RNA')
		datExpr <- GetDatExpr(test_seurat)

		check <- all(colnames(datExpr) %in% rownames(test_seurat))

		expect_equal(check, TRUE)

		})

		# check that the return_seurat flag works
		test_that("return_seurat flag works", {

		data(test_seurat)

		test_seurat <- SetupForWGCNA(
		test_seurat,
		wgcna_name = 'test',
		features = rownames(test_seurat)
		)

		test_seurat <- MetacellsByGroups(
		test_seurat,
		group.by = c('cell_type'),
		k = 5,
		max_shared = 5,
		ident.group = 'cell_type',
		target_metacells=50,
		min_cells=10
		)
		test_seurat <- NormalizeMetacells(test_seurat, verbose=FALSE)
		datExpr <- SetDatExpr(test_seurat, assay = 'RNA', return_seurat=FALSE)

		expect_equal(class(datExpr), "data.frame")
		})

		# check that the use_metacells flag works
		test_that("use_metacells flag works", {

		data(test_seurat)

		test_seurat <- SetupForWGCNA(
		test_seurat,
		wgcna_name = 'test',
		features = rownames(test_seurat)
		)

		test_seurat <- MetacellsByGroups(
		test_seurat,
		group.by = c('cell_type'),
		k = 5,
		max_shared = 5,
		ident.group = 'cell_type',
		target_metacells=50,
		min_cells=10
		)
		test_seurat <- NormalizeMetacells(test_seurat, verbose=FALSE)
		test_seurat <- SetDatExpr(test_seurat, assay = 'RNA', use_metacells=FALSE)
		datExpr <- GetDatExpr(test_seurat)

		check <- all(rownames(datExpr) %in% colnames(test_seurat))

		expect_equal(check, TRUE)
		})



		# test that group.by subsetting works as intended
		test_that("group.by subsetting works", {

		data(test_seurat)

		test_seurat <- SetupForWGCNA(
		test_seurat,
		wgcna_name = 'test',
		features = rownames(test_seurat)
		)

		test_seurat <- MetacellsByGroups(
		test_seurat,
		group.by = c('Sample'),
		k = 5,
		max_shared = 5,
		ident.group = 'Sample',
		target_metacells=10,
		min_cells=10
		)
		test_seurat <- NormalizeMetacells(test_seurat, verbose=FALSE)

		# selected groups to subset
		selected_groups <- c("C1", 'C2', 'C3')
		test_seurat <- SetDatExpr(
		test_seurat,
		group.by='Sample',
		group_name = selected_groups,
		assay = 'RNA'
		)
		datExpr <- GetDatExpr(test_seurat)

		# check that the groups are in the rownames of the datExpr
		samples <- do.call(rbind, strsplit(rownames(datExpr), '_'))[,1]
		check <- all(selected_groups %in% samples)

		expect_equal(check, TRUE)

		})
		No newline at end of file

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