Merge pull request satijalab#409 from satijalab/fix/subset_features

retain Graph and Neighbor objects when only subsetting features

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: Seurat
-Version: 3.2.1.9001
+Version: 3.2.1.9002
 Date: 2020-09-11
 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>, and Stuart T, Butler A, et al (2019) <doi:10.1016/j.cell.2019.05.031> for more details.

NEWS.md

@@ -7,6 +7,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 
 ### Changes
 - Set the seed in `WhichCells` regardless of whether or not `idents` is passed
+- Retain Graph and Neighbor objects when subsetting only on features
 
 ## [3.2.1] - 2020-09-04
 ### Added

R/objects.R

@@ -7349,6 +7349,10 @@ subset.Seurat <- function(x, subset, cells = NULL, features = NULL, idents = NUL
   if (all(cells %in% Cells(x = x)) && length(x = cells) == length(x = Cells(x = x)) && is.null(x = features)) {
     return(x)
   }
+  if (!all(colnames(x = x) %in% cells)) {
+    slot(object = x, name = 'graphs') <- list()
+    slot(object = x, name = 'neighbors') <- list()
+  }
   assays <- FilterObjects(object = x, classes.keep = 'Assay')
   # Filter Assay objects
   for (assay in assays) {
@@ -7394,8 +7398,6 @@ subset.Seurat <- function(x, subset, cells = NULL, features = NULL, idents = NUL
       x[[names(x = n.calc)]] <- n.calc
     }
   }
-  slot(object = x, name = 'graphs') <- list()
-  slot(object = x, name = 'neighbors') <- list()
   Idents(object = x, drop = TRUE) <- Idents(object = x)[cells]
   # subset images
   for (image in Images(object = x)) {