v2.6.1

ncborcherding · ncborcherding · commit 5eae8bd7dd21 · 2025-10-31T09:19:59.000-05:00
Small bug from GSVA in unit tests fix
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: escape
 Title: Easy single cell analysis platform for enrichment
-Version: 2.6.0
+Version: 2.6.1
 Authors@R: c(
     person(given = "Nick", family = "Borcherding", role = c("aut", "cre"), email = "ncborch@gmail.com"),
     person(given = "Jared", family = "Andrews", role = c("aut"), email = "jared.andrews07@gmail.com"),
diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,12 @@
+
+# 2.6.1
+
+Update to 2.6.0 to match Bioconductor Release 3.22 on 2025/10/30
+
+## BUG FIXES
+* Fixed issue `densityEnrichment()` interaction with GSVA package through the function `compute.gene.cdf`
+
+
 # 2.5.5  (2025-06-11)
 
 ## Bug fix & enhanced functionality
diff --git a/R/densityEnrichment.R b/R/densityEnrichment.R
@@ -67,7 +67,7 @@ densityEnrichment <- function(input.data,
     tmp  <- cnts[, cols, drop = FALSE]
     
     dens <- suppressWarnings(
-      compute.cdf(tmp, seq_len(ncol(tmp)), TRUE, FALSE)
+      compute.cdf(tmp, seq_len(ncol(tmp)), FALSE, FALSE)
     )
     ord  <- apply(dens, 2, order, decreasing = TRUE)          # genes × cells
     scores <- vapply(seq_len(ncol(ord)),
diff --git a/tests/testthat/test-densityEnrichment.R b/tests/testthat/test-densityEnrichment.R
@@ -7,7 +7,7 @@ GS    <- list(
 )
 
 # helper: number of groups in default 'ident' column
-n_groups <- length(unique(as.character(Idents(pbmc))))
+n_groups <- length(unique(as.character(SeuratObject::Idents(pbmc))))
 
 
 # ── 1  Core functionality returns patchwork object ──────────────────

Original file line number	Diff line number	Diff line change
`@@ -67,7 +67,7 @@ densityEnrichment <- function(input.data,`
`67`	`67`	`tmp <- cnts[, cols, drop = FALSE]`
`68`	`68`
`69`	`69`	`dens <- suppressWarnings(`
`70`		`- compute.cdf(tmp, seq_len(ncol(tmp)), TRUE, FALSE)`
	`70`	`+ compute.cdf(tmp, seq_len(ncol(tmp)), FALSE, FALSE)`
`71`	`71`	`)`
`72`	`72`	`ord <- apply(dens, 2, order, decreasing = TRUE) # genes × cells`
`73`	`73`	`scores <- vapply(seq_len(ncol(ord)),`
Original file line number	Diff line number	Diff line change
`@@ -7,7 +7,7 @@ GS <- list(`
`7`	`7`	`)`
`8`	`8`
`9`	`9`	`# helper: number of groups in default 'ident' column`
`10`		`-n_groups <- length(unique(as.character(Idents(pbmc))))`
	`10`	`+n_groups <- length(unique(as.character(SeuratObject::Idents(pbmc))))`
`11`	`11`
`12`	`12`
`13`	`13`	`# ── 1 Core functionality returns patchwork object ──────────────────`