# test that the output format is expected
test_that("SetDatExpr output is a data.frame", {
data(test_seurat)
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 <- 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)
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 <- 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)
})
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