Merge remote-tracking branch 'upstream/devel' into devel

Author: lcolladotor

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: derfinderPlot
 Type: Package
 Title: Plotting functions for derfinder
-Version: 1.41.0
-Date: 2021-11-22
+Version: 1.43.1
+Date: 2025-07-26
 Authors@R: c(person("Leonardo", "Collado-Torres", role = c("aut", "cre"), email
     = "lcolladotor@gmail.com", comment = c(ORCID = "0000-0003-2140-308X")),
     person(c("Andrew", "E."), "Jaffe", role = "aut",
@@ -13,7 +13,8 @@ Depends:
     R(>= 3.2)
 Imports:
     derfinder (>= 1.1.0),
-    GenomeInfoDb (>= 1.3.3),
+    Seqinfo,
+    GenomeInfoDb (>= 1.45.9),
     GenomicFeatures,
     GenomicRanges (>= 1.17.40),
     ggbio (>= 1.13.13),
@@ -51,6 +52,6 @@ LazyData: false
 URL: https://github.com/leekgroup/derfinderPlot
 BugReports: https://support.bioconductor.org/t/derfinderPlot
 biocViews: DifferentialExpression, Sequencing, RNASeq, Software, Visualization, ImmunoOncology
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.2
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)

NAMESPACE

@@ -5,21 +5,21 @@ export(plotOverview)
 export(plotRegionCoverage)
 export(vennRegions)
 import(S4Vectors)
-importFrom(GenomeInfoDb,'seqlengths<-')
-importFrom(GenomeInfoDb,'seqlevels<-')
 importFrom(GenomeInfoDb,getChromInfoFromUCSC)
 importFrom(GenomeInfoDb,mapSeqlevels)
 importFrom(GenomeInfoDb,renameSeqlevels)
-importFrom(GenomeInfoDb,seqlengths)
-importFrom(GenomeInfoDb,seqlevels)
-importFrom(GenomeInfoDb,seqlevelsInUse)
 importFrom(GenomicFeatures,exonsBy)
 importFrom(GenomicRanges,GRangesList)
-importFrom(GenomicRanges,seqinfo)
 importFrom(GenomicRanges,seqnames)
 importFrom(IRanges,resize)
 importFrom(IRanges,width)
 importFrom(RColorBrewer,brewer.pal)
+importFrom(Seqinfo,'seqlengths<-')
+importFrom(Seqinfo,'seqlevels<-')
+importFrom(Seqinfo,seqinfo)
+importFrom(Seqinfo,seqlengths)
+importFrom(Seqinfo,seqlevels)
+importFrom(Seqinfo,seqlevelsInUse)
 importFrom(derfinder,extendedMapSeqlevels)
 importFrom(ggbio,plotIdeogram)
 importFrom(ggbio,theme_tracks_sunset)

R/plotCluster.R

@@ -69,7 +69,8 @@
 #' guides scale_y_continuous geom_segment
 #' @importFrom plyr ddply summarise
 #' @importFrom scales log2_trans log_trans
-#' @importFrom GenomeInfoDb seqlevels renameSeqlevels
+#' @importFrom Seqinfo seqlevels
+#' @importFrom GenomeInfoDb renameSeqlevels
 #' @importFrom GenomicFeatures exonsBy
 #' @importFrom RColorBrewer brewer.pal
 #' @importFrom derfinder extendedMapSeqlevels

R/plotOverview.R

@@ -43,9 +43,8 @@
 #' @author Leonardo Collado-Torres
 #' @export
 #'
-#' @importFrom GenomicRanges seqinfo
-#' @importFrom GenomeInfoDb seqlengths 'seqlengths<-' seqlevels renameSeqlevels
-#' getChromInfoFromUCSC mapSeqlevels
+#' @importFrom Seqinfo seqinfo seqlengths 'seqlengths<-' seqlevels
+#' @importFrom GenomeInfoDb renameSeqlevels getChromInfoFromUCSC mapSeqlevels
 #' @importMethodsFrom ggbio autoplot layout_karyogram
 #' @importFrom ggplot2 aes labs scale_colour_manual scale_fill_manual geom_text
 #' rel geom_segment xlab theme element_text element_blank

R/plotRegionCoverage.R

@@ -44,8 +44,7 @@
 #' @importFrom GenomicRanges GRangesList
 #' @importMethodsFrom GenomicRanges names start end '$' as.data.frame
 #' gaps findOverlaps
-#' @importFrom GenomeInfoDb seqlengths 'seqlengths<-' 'seqlevels<-'
-#' seqlevelsInUse
+#' @importFrom Seqinfo seqlengths 'seqlengths<-' 'seqlevels<-' seqlevelsInUse
 #' @importFrom graphics abline axis layout legend matplot mtext par plot
 #' plot.new polygon text
 #' @importFrom grDevices devAskNewPage palette
@@ -72,7 +71,7 @@
 #' fullCov <- list("21" = genomeDataRaw$coverage)
 #'
 #' ## Assign chr lengths using hg19 information
-#' library("GenomicRanges")
+#' library("GenomeInfoDb")
 #' seqlengths(regions) <- seqlengths(getChromInfoFromUCSC("hg19",
 #'     as.Seqinfo = TRUE
 #' ))[