Merge pull request from satijalab/fix/dims_to_integrate

Stop dims.to.integrate from being overwritten

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: Seurat
-Version: 5.1.0.9015
+Version: 5.1.0.9016
 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(

NEWS.md

@@ -1,6 +1,7 @@
 # Unreleased
 
 ## Changes
+- Fixed `IntegrateLayers` to respect the `dims.to.integrate` parameter.
 - Added `stroke.size` parameter to `DimPlot` ([#8180](https://github.com/satijalab/seurat/pull/8180))
 - Updated `RunLeiden` to use the `leidenbase` package instead of `leiden`; deprecated the `method` parameter for `RunLeiden` and `FindClusters`; updated `RunLeiden` to reset `random.seed` to 1 if the value is 0 or less ([#6792](https://github.com/satijalab/seurat/pull/6792))
 - Updated `RunUMAP` to support `umap-learn` version >= 0.5.0 ([#9559](https://github.com/satijalab/seurat/pull/9559))

R/integration.R

@@ -1694,7 +1694,7 @@ IntegrateEmbeddings.IntegrationAnchorSet <- function(
         object = reference.integrated[[new.reduction.name.safe]]
       ))),
       assay = intdr.assay,
-      loadings = Loadings(object = reductions),
+      loadings = Loadings(object = reductions)[,dims.to.integrate],
       key = paste0(new.reduction.name.safe, "_")
     )
     DefaultAssay(object = reference.integrated) <- int.assay
@@ -6319,8 +6319,9 @@ ValidateParams_IntegrateEmbeddings_IntegrationAnchors <- function(
       warning("Max dims.to.integrate is larger than the number of dimensions in ",
               "the provided reduction. Setting dims.to.integrate to 1:",
               ncol(x = reductions), " and continuing.", immediate. = TRUE, call. = FALSE)
+      dims.to.integrate <- 1:ncol(x = reductions)
     }
-    ModifyParam(param = 'dims.to.integrate', value = 1:ncol(x = reductions))
+    ModifyParam(param = 'dims.to.integrate', value = dims.to.integrate)
   }
   if (!is.null(x = weight.reduction)) {
     if (inherits(x = weight.reduction, what = "character")) {

tests/testthat/test_integration5.R

@@ -95,6 +95,43 @@ test_that("IntegrateLayers works with CCAIntegration", {
     Embeddings(integrated[["integrated"]])[75, 45],
     0.5442
   )
+
+  integrated_sub <- suppressWarnings(
+    IntegrateLayers(
+      test.data.std,
+      method = CCAIntegration,
+      orig.reduction = "pca",
+      new.reduction = "integrated",
+      verbose = FALSE,
+      # since `k.weight` must be less than the number of samples in the
+      # smallest layer being integrated, it must be set to accommodate the
+      # small dataset used for testing
+      k.weight = 10,
+      dims.to.integrate = 1:10
+    )
+  )
+  # check that the integrated reduction has the specified number of
+  # `dims.to.integrate`
+  expect_equal(ncol(integrated_sub[["integrated"]]), 10)
+
+  integrated_overflow <- suppressWarnings(
+    IntegrateLayers(
+      test.data.std,
+      method = CCAIntegration,
+      orig.reduction = "pca",
+      new.reduction = "integrated",
+      verbose = FALSE,
+      # since `k.weight` must be less than the number of samples in the
+      # smallest layer being integrated, it must be set to accommodate the
+      # small dataset used for testing
+      k.weight = 10,
+      dims.to.integrate = 1:100
+    )
+  )
+  # check that the integrated reduction is the same as you'd get if you
+  # didn't specify `dims.to.integrate` (i.e. the same size as the initial
+  # reduction)
+  expect_equal(Embeddings(integrated_overflow), Embeddings(integrated))
 })
 
 test_that("IntegrateLayers works with RPCAIntegration", {
@@ -127,6 +164,44 @@ test_that("IntegrateLayers works with RPCAIntegration", {
     Embeddings(integrated[["integrated"]])[75, 45],
     0.5442
   )
+
+  # check that the integrated reduction has the specified number of
+  # `dims.to.integrate`
+  integrated_sub <- suppressWarnings(
+    IntegrateLayers(
+      test.data.std,
+      method = RPCAIntegration,
+      orig.reduction = "pca",
+      new.reduction = "integrated",
+      verbose = FALSE,
+      # since `k.weight` must be less than the number of samples in the
+      # smallest layer being integrated, it must be set to accommodate the
+      # small dataset used for testing
+      k.weight = 10,
+      dims.to.integrate = 1:10
+    )
+  )
+  # check that dims.to.integrate is not being overwritten
+  expect_equal(ncol(integrated_sub[["integrated"]]), 10)
+
+  integrated_overflow <- suppressWarnings(
+    IntegrateLayers(
+      test.data.std,
+      method = RPCAIntegration,
+      orig.reduction = "pca",
+      new.reduction = "integrated",
+      verbose = FALSE,
+      # since `k.weight` must be less than the number of samples in the
+      # smallest layer being integrated, it must be set to accommodate the
+      # small dataset used for testing
+      k.weight = 10,
+      dims.to.integrate = 1:100
+    )
+  )
+  # check that the integrated reduction is the same as you'd get if you
+  # didn't specify `dims.to.integrate` (i.e. the same size as the initial
+  # reduction)
+  expect_equal(Embeddings(integrated_overflow), Embeddings(integrated))
 })
 
 test_that("IntegrateLayers works with JointPCAIntegration", {
@@ -159,6 +234,43 @@ test_that("IntegrateLayers works with JointPCAIntegration", {
     Embeddings(integrated[["integrated"]])[75, 45],
     0.5442
   )
+  # check that the integrated reduction has the specified number of
+  # `dims.to.integrate`
+  integrated_sub <- suppressWarnings(
+    IntegrateLayers(
+      test.data.std,
+      method = JointPCAIntegration,
+      orig.reduction = "pca",
+      new.reduction = "integrated",
+      verbose = FALSE,
+      # since `k.weight` must be less than the number of samples in the
+      # smallest layer being integrated, it must be set to accommodate the
+      # small dataset used for testing
+      k.weight = 10,
+      dims.to.integrate = 1:10
+    )
+  )
+  # check that dims.to.integrate is not being overwritten
+  expect_equal(ncol(integrated_sub[["integrated"]]), 10)
+
+  integrated_overflow <- suppressWarnings(
+    IntegrateLayers(
+      test.data.std,
+      method = JointPCAIntegration,
+      orig.reduction = "pca",
+      new.reduction = "integrated",
+      verbose = FALSE,
+      # since `k.weight` must be less than the number of samples in the
+      # smallest layer being integrated, it must be set to accommodate the
+      # small dataset used for testing
+      k.weight = 10,
+      dims.to.integrate = 1:100
+    )
+  )
+  # check that the integrated reduction is the same as you'd get if you
+  # didn't specify `dims.to.integrate` (i.e. the same size as the initial
+  # reduction)
+  expect_equal(Embeddings(integrated_overflow), Embeddings(integrated))
 })
 
 test_that("IntegrateLayers fails when expected", {