Update tests

stuart-lab · Jan 16, 2025 · 1eb526c · 1eb526c
1 parent 6a720d5
commit 1eb526c
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Showing 2 changed files with 52 additions and 48 deletions.
diff --git a/tests/testthat/test-motifs.R b/tests/testthat/test-motifs.R
@@ -2,16 +2,17 @@ pwm <- readRDS("../testdata/pwm_2motifs.rds")
 genome.fasta <- system.file("extdata", "chr1_start.fa", package = "Signac")
 genome <- Rsamtools::FaFile(genome.fasta)
 
-# Cannot be tested if motifmatchr is not a dependency
-# test_that("AddMotifs works", {
-#   motif <- AddMotifs(
-#     atac_small[["peaks"]],
-#     genome,
-#     pwm,
-#     verbose = FALSE
-#   )
-#   expect_equal(dim(Motifs(motif)), c(323, 2))
-# })
+
+test_that("AddMotifs works", {
+  skip_if_not_installed("motifmatchr")
+  motif <- AddMotifs(
+    atac_small[["peaks"]],
+    genome,
+    pwm,
+    verbose = FALSE
+  )
+  expect_equal(dim(Motifs(motif)), c(323, 2))
+})
 
 test_that("AddMotifs works with fakechr", {
   fpath <- system.file("extdata", "fragments.tsv.gz", package = "Signac")
@@ -29,35 +30,35 @@ test_that("AddMotifs works with fakechr", {
     keep_all_features = TRUE,
     verbose = FALSE
   )
-  object <- CreateChromatinAssay(
+  expect_warning(object <- CreateChromatinAssay(
     counts = mat,
     sep = c(":", "-"),
     fragments = fragments,
     verbose = FALSE
-  )
-  # This requires motifmatchr
-  # motif <- AddMotifs.default(
-  #   granges(object)[100:nrow(object)],
-  #   genome,
-  #   pwm,
-  #   verbose = FALSE
-  # )
+  ))
+  skip_if_not_installed("motifmatchr")
+  motif <- suppressWarnings(AddMotifs(
+    granges(object)[100:nrow(object)],
+    genome,
+    pwm,
+    verbose = FALSE
+  ))
   motif <- readRDS("../testdata/motifObj_2_225.rds")
   expect_equal(dim(motif), c(225, 2))
-  test <- SetAssayData(
+  expect_warning(test <- SetAssayData(
     object = object,
     layer = "motifs",
     new.data = motif,
     verbose = FALSE
-  )
+  ))
   expect_equal(dim(Motifs(test)), c(324, 2))
   # If some features are not in the ChromatinAssay
   # They should be removed
-  test <- SetAssayData(
+  expect_warning(test <- SetAssayData(
     object = atac_small,
     layer = "motifs",
     new.data = motif,
     verbose = FALSE
-  )
+  ))
   expect_equal(dim(Motifs(test)), c(323, 2))
 })
diff --git a/tests/testthat/test-preprocessing.R b/tests/testthat/test-preprocessing.R
@@ -105,28 +105,31 @@ test_that("NucleosomeSignal works", {
     expected = c(NaN, NaN, 0.0, 2.5, NaN, NaN)
   )
 })
-# Cannot be tested if motifmatchr is not a dependency
-# test_that("CreateMotifMatrix works", {
-#   pwm <- readRDS("../testdata/pwm_2motifs.rds")
-#   genome.fasta <- system.file("extdata", "chr1_start.fa", package = "Signac")
-#   genome <- Rsamtools::FaFile(genome.fasta)
-#   motif.matrix <- CreateMotifMatrix(
-#     features = granges(atac_small),
-#     pwm = pwm,
-#     genome = genome
-#   )
-#   expect_equal(dim(motif.matrix), c(323, 2))
-#   features <- suppressWarnings(c(
-#     granges(atac_small),
-#     GenomicRanges::GRanges(
-#       seqnames = "fake_chr",
-#       ranges = IRanges::IRanges(start = 1, end = 1000)
-#     )
-#   ))
-#   motif.matrix <- CreateMotifMatrix(
-#     features = features,
-#     pwm = pwm,
-#     genome = BSgenome.Hsapiens.UCSC.hg19
-#   )
-#   expect_equal(dim(motif.matrix), c(324, 2))
-# })
+
+
+test_that("CreateMotifMatrix works", {
+  pwm <- readRDS("../testdata/pwm_2motifs.rds")
+  genome.fasta <- system.file("extdata", "chr1_start.fa", package = "Signac")
+  genome <- Rsamtools::FaFile(genome.fasta)
+  skip_if_not_installed("motifmatchr")
+  motif.matrix <- suppressWarnings(CreateMotifMatrix(
+    features = granges(atac_small),
+    pwm = pwm,
+    genome = genome
+  ))
+  expect_equal(dim(motif.matrix), c(323, 2))
+  features <- suppressWarnings(c(
+    granges(atac_small),
+    GenomicRanges::GRanges(
+      seqnames = "fake_chr",
+      ranges = IRanges::IRanges(start = 1, end = 1000)
+    )
+  ))
+  skip_if_not_installed("BSgenome.Hsapiens.UCSC.hg19")
+  motif.matrix <- suppressWarnings(CreateMotifMatrix(
+    features = features,
+    pwm = pwm,
+    genome = BSgenome.Hsapiens.UCSC.hg19::BSgenome.Hsapiens.UCSC.hg19
+  ))
+  expect_equal(dim(motif.matrix), c(324, 2))
+})