Set umap nthreads to nthreads of BPPARAM

alanocallaghan · Mar 7, 2025 · 68425da · 68425da
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -12,8 +12,8 @@ Authors@R: c(
         person("Leo", "Lahti", role=c("ctb"), email="leo.lahti@utu.fi", comment = c(ORCID = "0000-0001-5537-637X")),
         person("Tuomas", "Borman", role = c("ctb"), comment = c(ORCID = "0000-0002-8563-8884"))
     )
-Version: 1.35.3
-Date: 2025-03-03
+Version: 1.35.4
+Date: 2025-03-07
 License: GPL-3
 Title: Single-Cell Analysis Toolkit for Gene Expression Data in R
 Description: A collection of tools for doing various analyses of

diff --git a/R/runUMAP.R b/R/runUMAP.R
@@ -64,10 +64,10 @@
 NULL
 
 #' @importFrom BiocNeighbors findKNN KmknnParam
-#' @importFrom BiocParallel SerialParam
+#' @importFrom BiocParallel SerialParam bpnworkers
 .calculate_umap <- function(x, ncomponents = 2, ntop = 500, 
     subset_row = NULL, scale=FALSE, transposed=FALSE, pca=if (transposed) NULL else 50,
-    n_neighbors=15, n_threads=NULL, ..., 
+    n_neighbors=15, n_threads=bpnworkers(BPPARAM), ..., 
     external_neighbors=FALSE, BNPARAM = KmknnParam(), BPPARAM = SerialParam(),
     use_densvis=FALSE, dens_frac = 0.3, dens_lambda = 0.1)
 {

diff --git a/man/runUMAP.Rd b/man/runUMAP.Rd