From 53084272edd02160fd87385b969b5a5fcbe40c3b Mon Sep 17 00:00:00 2001 From: Liripo <54770415+Liripo@users.noreply.github.com> Date: Thu, 25 Jul 2024 10:28:41 +0800 Subject: [PATCH 1/2] Update DESCRIPTION ComplexHeatmap is bioconductor package, should added biocViews field to download. --- DESCRIPTION | 1 + 1 file changed, 1 insertion(+) diff --git a/DESCRIPTION b/DESCRIPTION index fa8b685..1432140 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -9,6 +9,7 @@ Depends: R (>= 3.6.0),dplyr,igraph,ggplot2 License: GPL-3 Encoding: UTF-8 LazyData: TRUE +biocViews: Software, Visualization Imports: future, future.apply, From b34846e5a8aa26638083d6d72c94b5a926c1d840 Mon Sep 17 00:00:00 2001 From: Liripo Date: Thu, 25 Jul 2024 18:25:32 +0800 Subject: [PATCH 2/2] Update identifyOverExpressedGenes Sparse matrices can be used when using `Presto`, and are much faster --- R/utilities.R | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/R/utilities.R b/R/utilities.R index fdc4a59..a2043f0 100644 --- a/R/utilities.R +++ b/R/utilities.R @@ -396,7 +396,6 @@ identifyOverExpressedGenes <- function(object, data.use = NULL, group.by = NULL, if (do.DE) { # select genes based on differential expression - data.use <- as.matrix(data.use) if (is.null(group.by)) { labels <- object@idents @@ -495,7 +494,7 @@ identifyOverExpressedGenes <- function(object, data.use = NULL, group.by = NULL, object@var.features[[features.name]] <- markers.all } else { - + data.use <- as.matrix(data.use) my.sapply <- ifelse( test = future::nbrOfWorkers() == 1, yes = pbapply::pbsapply,