Merge pull request #601 from satijalab/fix/lsiproject_center

not center query lsi embeddings
satijalab · Oct 8, 2021 · 1d1b139 · 1d1b139
2 parents 4ffdad4 + 297764c
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: Seurat
-Version: 4.0.4.9002
-Date: 2021-09-10 
+Version: 4.0.4.9003
+Date: 2021-10-07
 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/NEWS.md b/NEWS.md
@@ -13,6 +13,7 @@
 - Add `ReadParsebio()` function to read output from Parse Biosciences
 - 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))
+- Set `do.center` to FALSE for `lsiproject` in `FindTransferAnchors` 
 
 ## Changes
 - Warn and continue rather than erroring if not all features are available in `FindSpatiallyVariableFeatures()` ([#4611](https://github.com/satijalab/seurat/issues/4611))

diff --git a/R/integration.R b/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