Merge pull request #454 from satijalab/fix/mapping_score_k

fix bugs in mapping score precomputed neighbors
satijalab · Oct 27, 2020 · a89047d · a89047d
2 parents 5f5ad30 + e83012f
commit a89047d
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: Seurat
-Version: 3.9.9.9006
-Date: 2020-10-25
+Version: 3.9.9.9007
+Date: 2020-10-27
 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.
 Authors@R: c(

diff --git a/R/integration.R b/R/integration.R
@@ -845,7 +845,7 @@ FindTransferAnchors <- function(
   )
   if (!is.null(x = precomputed.neighbors[["query.neighbors"]])) {
     slot(object = anchor.set, name = "neighbors") <- list(
-      query.neighbors = precomputed.neighbors[["query.neighbors"]])
+      query.neighbors = query.neighbors)
   }
   return(anchor.set)
 }
@@ -1620,7 +1620,7 @@ MappingScore.default <- function(
   CheckDots(...)
   # Input checks
   start.time <- Sys.time()
-  if (ncol(x = query.neighbors) < ksmooth) {
+  if (is.null(x = query.neighbors) || ncol(x = query.neighbors) < ksmooth) {
     message("Recomputing query neighborhoods.\nSetting mapping.score.k in ",
             "FindTransferAnchors to the ksmooth \nvalue here (",
             ksmooth, "), can bypass this calculation in future runs.")