merge

tsjzz · Jul 16, 2021 · 32f83c1 · 32f83c1
2 parents dd80ff6 + fb0394a
commit 32f83c1
Show file tree

Hide file tree

Showing 3 changed files with 5 additions and 1 deletion.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: Seurat
 Version: 4.0.3.9010
-Date: 2021-07-12
+Date: 2021-07-16
 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 @@
 - Bug fix for reading from absolute paths in ReadMtx ([#4723](https://github.com/satijalab/seurat/issues/4723)) 
 - Bug fix in SingleCellExperiment conversion ([#4633](https://github.com/satijalab/seurat/issues/4633))
 - Bug fix in `FindVariableFeatures()` when using `selection.method = "mvp"` and `binning.method = "equal_frequency"` ([#4712](https://github.com/satijalab/seurat/issues/4712))
+- Fix cell renaming in `RunCCA()`
 
 ## Seurat 4.0.3 (2020-06-10)`
 ## Added

diff --git a/R/dimensional_reduction.R b/R/dimensional_reduction.R
@@ -635,6 +635,9 @@ RunCCA.Seurat <- function(
     merge.data = TRUE,
     ...
   )
+  rownames(x = cca.results$ccv) <- Cells(x = combined.object)
+  colnames(x = data1) <- Cells(x = combined.object)[1:ncol(x = data1)]
+  colnames(x = data2) <- Cells(x = combined.object)[(ncol(x = data1) + 1):length(x = Cells(x = combined.object))]
   combined.object[['cca']] <- CreateDimReducObject(
     embeddings = cca.results$ccv[colnames(combined.object), ],
     assay = assay1,