Merge branch 'develop' of github.com:satijalab/seurat-private into de…

…velop

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: Seurat
-Version: 4.0.5
-Date: 2021-10-04
+Version: 4.0.5.9000
+Date: 2021-10-19
 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

@@ -1,3 +1,9 @@
+# Unreleased
+## Added
+
+## Changes
+- Set `do.center` to FALSE for `lsiproject` in `FindTransferAnchors`
+
 # Seurat 4.0.5 (2020-10-04)
 ## Changes
 - Update documentation for `to.upper` parameter in `Load10X_Spatial()` ([#4576](https://github.com/satijalab/seurat/issues/4576))
@@ -15,6 +21,7 @@
 - Add the `image.alpha` parameter to `SpatialDimPlot()` and `SpatialFeaturePlot()`
 - Add support for the correlation metric in `RunUMAP` ([#4972](https://github.com/satijalab/seurat/issues/4972))
 
+
 ## Changes
 - Warn and continue rather than erroring if not all features are available in `FindSpatiallyVariableFeatures()` ([#4611](https://github.com/satijalab/seurat/issues/4611))
 - Bug fix for SCT-based integration in selecting proper reference model ([#4355](https://github.com/satijalab/seurat/issues/4355))

R/integration.R

@@ -1041,7 +1041,7 @@ FindTransferAnchors <- function(
         reduction = query[[reference.reduction]],
         data = GetAssayData(object = reference, assay = reference.assay, slot = "data"),
         mode = "lsi",
-        do.center = TRUE,
+        do.center = FALSE,
         do.scale = FALSE,
         use.original.stats = FALSE,
         verbose = verbose
@@ -1053,7 +1053,7 @@ FindTransferAnchors <- function(
         reduction = reference[[reference.reduction]],
         data = GetAssayData(object = query, assay = query.assay, slot = "data"),
         mode = "lsi",
-        do.center = TRUE,
+        do.center = FALSE,
         do.scale = FALSE,
         use.original.stats = FALSE,
         verbose = verbose