Merge pull request satijalab#898 from satijalab/fix/test_integration

Improve tests for IntegrateLayers
10XGenomics · Feb 14, 2024 · 942766a · 942766a
2 parents 150a85b + 120265e
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: Seurat
-Version: 5.0.1.9006
-Date: 2024-02-07
+Version: 5.0.1.9007
+Date: 2024-02-13
 Title: Tools for Single Cell Genomics
 Description: A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. 'Seurat' aims to enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. See Satija R, Farrell J, Gennert D, et al (2015) <doi:10.1038/nbt.3192>, Macosko E, Basu A, Satija R, et al (2015) <doi:10.1016/j.cell.2015.05.002>, Stuart T, Butler A, et al (2019) <doi:10.1016/j.cell.2019.05.031>, and Hao, Hao, et al (2020) <doi:10.1101/2020.10.12.335331> for more details.
 Authors@R: c(

diff --git a/tests/testthat/test_integratedata.R b/tests/testthat/test_integratedata.R
@@ -111,99 +111,4 @@ test_that("Input validates correctly ", {
   skip_on_cran()
   #expect_warning(IntegrateData(anchorset = anchors2, k.weight = 50, features = c(rownames(ref), "BAD")))
   #expect_warning(IntegrateData(anchorset = anchors2, k.weight = 50, dims = 1:1000))
-})
-
-# Tests for IntegrateLayers
-# ------------------------------------------------------------------------------
-context("IntegrateLayers")
-pbmc_small[['RNAv5']] <- CreateAssay5Object(counts = LayerData(pbmc_small[['RNA']], layer = "counts"))
-
-pbmc_small[["RNAv5"]] <- split(pbmc_small[["RNAv5"]], f = pbmc_small$groups)
-DefaultAssay(pbmc_small) <- "RNAv5"
-pbmc_small <- NormalizeData(pbmc_small)
-pbmc_small <- FindVariableFeatures(pbmc_small)
-pbmc_small <- ScaleData(pbmc_small)
-pbmc_small <- suppressMessages(suppressWarnings(RunPCA(pbmc_small)))
-
-
-test_that("IntegrateLayers does not work on a v3 assay ", {
-  expect_error(IntegrateLayers(object = pbmc_small, method = CCAIntegration,
-                               orig.reduction = "pca",
-                               assay = "RNA",
-                               new.reduction = "integrated.cca"))
-})
-
-test_that("IntegrateLayers errors out if incorrect input ", {
-  expect_error(IntegrateLayers(object = pbmc_small, method = CCAIntegration,
-                               orig.reduction = "pca",
-                               assay = "DNA",
-                               new.reduction = "integrated.cca"))
-  expect_error(IntegrateLayers(object = pbmc_small, method = CCAIntegration,
-                               orig.reduction = "lda",
-                               new.reduction = "integrated.cca"))
-})
-
-#itegration methods
-int_cca <- suppressMessages(suppressWarnings(IntegrateLayers(
-  object = pbmc_small, method = CCAIntegration,
-  orig.reduction = "pca", new.reduction = "integrated.cca",
-  k.weight=25,
-  verbose = FALSE
-)))
-int_rpca <- suppressMessages(suppressWarnings(IntegrateLayers(
-  object = pbmc_small, method = RPCAIntegration,
-  orig.reduction = "pca", new.reduction = "integrated.rpca",
-  dims = 1:10,
-  k.anchor = 10,
-  k.weight=10,
-  verbose = FALSE
-)))
-
-# int_mnn <- suppressMessages(suppressWarnings(IntegrateLayers(
-#   object = pbmc_small, method = FastMNNIntegration,
-#   new.reduction = "integrated.mnn",
-#   k.weight=25,
-#   verbose = FALSE
-# )))
-
-
-test_that("IntegrateLayers returns embeddings with correct dimensions ", {
-  expect_equal(dim(int_cca[["integrated.cca"]]), c(80, 50))
-  expect_equal(dim(int_rpca[["integrated.rpca"]]), c(80, 50))
-
-  int_rpca
-  expect_equal(int_cca[["integrated.cca"]]@assay.used, "RNAv5")
-  #expect_equal(int_cca[['integrated.cca']]@cell.embeddings, c(3, 4, 5))
-})
-
-test_that("IntegrateLayers works with harmony", {
-  skip_on_cran()
-  skip_if_not_installed("harmony")
-  int_harmony <- suppressMessages(suppressWarnings(IntegrateLayers(
-    object = pbmc_small, method = HarmonyIntegration,
-    orig.reduction = "pca", new.reduction = "harmony",
-    k.weight=25,
-    verbose = FALSE
-  )))
-  expect_equal(dim(int_harmony[["harmony"]]), c(80, 50))
-
-
-})
-
-test_that("group.by ", {
-  expect_equal(dim(int_cca[["integrated.cca"]]), c(80, 50))
-  expect_equal(int_cca[["integrated.cca"]]@assay.used, "RNAv5")
-})
-
-
-#Harmony integration
-# int_2 <- IntegrateLayers(object = pbmc_small, method = CCAIntegration,
-#                          group.by = "letter.idents",
-#                 orig.reduction = "pca",
-#                 assay = "RNAv5",
-#                 k.weight = 20,
-#                 new.reduction = "integrated.cca")
-#
-# head(int_2[['integrated.cca']]@cell.embeddings[1:5,1:5])
-# head(int_cca[['integrated.cca']]@cell.embeddings[1:5,1:5])
-
+})