Fix bug

showteeth · showteeth · commit eb0b3c3e3e78 · 2022-07-23T22:25:50.000+08:00
diff --git a/NAMESPACE b/NAMESPACE
@@ -21,6 +21,7 @@ importFrom(Biostrings,letterFrequency)
 importFrom(Biostrings,readDNAStringSet)
 importFrom(GenomeInfoDb,"seqlengths<-")
 importFrom(GenomeInfoDb,seqlengths)
+importFrom(GenomeInfoDb,seqnames)
 importFrom(GenomicRanges,GRanges)
 importFrom(GenomicRanges,makeGRangesFromDataFrame)
 importFrom(GenomicRanges,setdiff)
diff --git a/R/geom_ideogram.R b/R/geom_ideogram.R
@@ -21,7 +21,7 @@
 #' @importFrom patchwork wrap_plots
 #' @importFrom methods extends
 #' @importFrom utils menu
-#' @importFrom GenomeInfoDb seqlengths seqlengths<-
+#' @importFrom GenomeInfoDb seqlengths seqlengths<- seqnames
 #' @importFrom GenomicRanges trim
 #' @importFrom S4Vectors values<-
 #' @export
diff --git a/R/utils.R b/R/utils.R
@@ -222,7 +222,7 @@ getIdeogram <- function(genome, subchr = NULL, cytobands = TRUE) {
       message("Done")
     }
     if (length(subchr)) {
-      gr <- gr[seqnames(gr) == subchr]
+      gr <- gr[GenomeInfoDb::seqnames(gr) == subchr]
     }
 
     gr <- sort(gr)

Original file line number	Diff line number	Diff line change
`@@ -222,7 +222,7 @@ getIdeogram <- function(genome, subchr = NULL, cytobands = TRUE) {`
`222`	`222`	`message("Done")`
`223`	`223`	`}`
`224`	`224`	`if (length(subchr)) {`
`225`		`- gr <- gr[seqnames(gr) == subchr]`
	`225`	`+ gr <- gr[GenomeInfoDb::seqnames(gr) == subchr]`
`226`	`226`	`}`
`227`	`227`
`228`	`228`	`gr <- sort(gr)`