merge fix

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: Seurat
-Version: 4.2.1.9001
-Date: 2022-11-09
+Version: 4.3.0
+Date: 2022-11-18
 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(
@@ -10,8 +10,10 @@ Authors@R: c(
   person(given = "Jeff", family = "Farrell", email = "[email protected]", role = "ctb"),
   person(given = "Christoph", family = "Hafemeister", email = "[email protected]", role = "ctb", comment = c(ORCID = "0000-0001-6365-8254")),
   person(given = "Yuhan", family = "Hao", email = "[email protected]", role = "ctb", comment = c(ORCID = "0000-0002-1810-0822")),
+  person(given = "Austin", family = "Hartman", email = "[email protected]", role = "ctb", comment = c(ORCID = "0000-0001-7278-1852")),
   person(given = "Paul", family = "Hoffman", email = "[email protected]", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-7693-8957")),
   person(given = "Jaison", family = "Jain", email = "[email protected]", role = "ctb", comment = c(ORCID = "0000-0002-9478-5018")),
+  person(given = "Madeline", family = "Kowalski", email = "[email protected]", role = "ctb", comment = c(ORCID = "0000-0002-5655-7620")),
   person(given = "Efthymia", family = "Papalexi", email = "[email protected]", role = "ctb", comment = c(ORCID = "0000-0001-5898-694X")),
   person(given = "Patrick", family = "Roelli", email = "[email protected]", role = "ctb"),
   person(given = "Rahul", family = "Satija", email = "[email protected]", role = "ctb", comment = c(ORCID = "0000-0001-9448-8833")),
@@ -96,7 +98,7 @@ Collate:
     'tree.R'
     'utilities.R'
     'zzz.R'
-RoxygenNote: 7.2.1
+RoxygenNote: 7.2.2
 Encoding: UTF-8
 Suggests:
     ape,

NEWS.md

@@ -1,4 +1,12 @@
-# Seurat 4.2.1 (2022-11-07)
+# Seurat 4.3.0 (2022-11-18)
+
+## Added
+- Add support for imaging-based spatial datasets
+
+## Changes
+- Fix bug in `FindMarkers()` when run post Integration/Transfer ([#6856](https://github.com/satijalab/seurat/issues/6586))
+
+# Seurat 4.2.1 (2022-11-08)
 
 ## Changes
 - Replaced import from `spatstat.core` with `spatstat.explore`

R/differential_expression.R

@@ -989,9 +989,16 @@ FindMarkers.Seurat <- function(
       command = norm.command,
       value = "normalization.method"
     )
-  } else {
+  } else if (length(x = intersect(x = c("FindIntegrationAnchors", "FindTransferAnchors"), y = Command(object = object)))) {
+    command <- intersect(x = c("FindIntegrationAnchors", "FindTransferAnchors"), y = Command(object = object))[1]
+    Command(
+      object = object,
+      command = command,
+      value = "normalization.method"
+      )
+    } else {
     NULL
-  }
+    }
   de.results <- FindMarkers(
     object = data.use,
     slot = slot,

tests/testthat/test_differential_expression.R

@@ -326,6 +326,34 @@ test_that("FindAllMarkers works as expected", {
   expect_equal(rownames(results.pseudo)[1], "HLA-DPB1")
 })
 
+
+# Tests for running FindMarkers post integration/transfer
+ref <- pbmc_small
+ref <- FindVariableFeatures(object = ref, verbose = FALSE, nfeatures = 100)
+query <- CreateSeuratObject(
+  counts = GetAssayData(object = pbmc_small[['RNA']], slot = "counts") + rpois(n = ncol(pbmc_small), lambda = 1)
+)
+query2 <- CreateSeuratObject(
+  counts = GetAssayData(object = pbmc_small[['RNA']], slot = "counts")[, 1:40] + rpois(n = ncol(pbmc_small), lambda = 1)
+)
+query.list <- list(query, query2)
+query.list <- lapply(X = query.list, FUN = NormalizeData, verbose = FALSE)
+query.list <- lapply(X = query.list, FUN = FindVariableFeatures, verbose = FALSE, nfeatures = 100)
+query.list <- lapply(X = query.list, FUN = ScaleData, verbose = FALSE)
+query.list <- suppressWarnings(lapply(X = query.list, FUN = RunPCA, verbose = FALSE, npcs = 20))
+
+anchors <- suppressMessages(suppressWarnings(FindIntegrationAnchors(object.list = c(ref, query.list), k.filter = NA, verbose = FALSE)))
+object <- suppressMessages(IntegrateData(anchorset = anchors,  k.weight = 25, verbose = FALSE))
+object <- suppressMessages(ScaleData(object, verbose = FALSE))
+object <- suppressMessages(RunPCA(object, verbose = FALSE))
+object <- suppressMessages(FindNeighbors(object = object, verbose = FALSE))
+object <- suppressMessages(FindClusters(object, verbose = FALSE))
+markers <- FindMarkers(object = object, ident.1="0", ident.2="1")
+test_that("FindMarkers recognizes log normalizatio", {
+  expect_equal(markers[1, "p_val"], 1.598053e-14)
+  expect_equal(markers[1, "avg_log2FC"], -2.614686, tolerance = 1e-6)
+})
+
 # Tests for FindConservedMarkers
 # -------------------------------------------------------------------------------