fix: update to fetch USCS cytoband info, closes #19

showteeth · May 13, 2024 · 5234de3 · 5234de3
1 parent 3984adf
commit 5234de3
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Showing 3 changed files with 8 additions and 23 deletions.
diff --git a/NAMESPACE b/NAMESPACE
@@ -55,6 +55,7 @@ importFrom(Biostrings,readAAStringSet)
 importFrom(Biostrings,readDNAStringSet)
 importFrom(Biostrings,translate)
 importFrom(GenomeInfoDb,"seqlengths<-")
+importFrom(GenomeInfoDb,genome)
 importFrom(GenomeInfoDb,seqlengths)
 importFrom(GenomeInfoDb,seqnames)
 importFrom(GenomicAlignments,alphabetFrequencyFromBam)

diff --git a/R/geom_ideogram.R b/R/geom_ideogram.R
@@ -31,7 +31,7 @@
 #' @importFrom utils menu
 #' @importFrom rtracklayer ucscGenomes ucscTableQuery tableName getTable
 #'   GRangesForUCSCGenome browserSession
-#' @importFrom GenomeInfoDb seqlengths seqlengths<- seqnames
+#' @importFrom GenomeInfoDb seqlengths genome seqlengths<- seqnames
 #' @export
 #'
 #' @examples
@@ -95,22 +95,6 @@ geom_ideogram <- function(genome = "hg19", mark.color = "red", mark.alpha = 0.7,
 
 #' @export
 ggplot_add.ideogram <- function(object, plot, object_name) {
-  # if (length(plot$layers) == 0) {
-  #   # geom_base
-  #   # get plot data
-  #   plot.data <- plot[[1]]$layers[[1]]$data
-  #   # prepare plot range
-  #   plot.chr <- as.character(plot.data[1, "seqnames"])
-  #   plot.region.start <- plot.data[1, "start"]
-  #   plot.region.end <- plot.data[nrow(plot.data), "end"]
-  # } else {
-  #   # get plot data
-  #   plot.data <- plot$layers[[1]]$data
-  #   # prepare plot range
-  #   plot.chr <- as.character(plot.data[1, "seqnames"])
-  #   plot.region.start <- plot$coordinates$limits$x[1]
-  #   plot.region.end <- plot$coordinates$limits$x[2]
-  # }
   # get plot data, plot data should contain bins
   if ("patchwork" %in% class(plot)) {
     plot.data <- plot[[1]]$layers[[1]]$data
@@ -146,7 +130,7 @@ ggplot_add.ideogram <- function(object, plot, object_name) {
   plot.height <- object$plot.height
 
   # get genome and chr ideogram
-  genome.info <- suppressWarnings(getIdeogram(genome = genome, subchr = plot.chr, cytobands = TRUE))
+  genome.info <- suppressWarnings(getIdeogram(genomes = genome, subchr = plot.chr, cytobands = TRUE))
   genome.info.df <- genome.info %>% as.data.frame()
   # get genome length
   genome.length <- genome.info.df[nrow(genome.info.df), "end"]

diff --git a/R/utils.R b/R/utils.R
@@ -242,9 +242,8 @@ SplitTxExonUTR <- function(exon.df, utr.df) {
 # From: https://github.com/jorainer/biovizBase/blob/master/R/ideogram.R
 # Fix bug: the names on the supplied 'seqlengths' vector must be
 # identical to the seqnames
-getIdeogram <- function(genome, subchr = NULL, cytobands = TRUE) {
-  .gnm <- genome
-  lst <- lapply(.gnm, function(genome) {
+getIdeogram <- function(genomes, subchr = NULL, cytobands = TRUE) {
+  lst <- lapply(genomes, function(genome) {
     if (!(exists("session") && extends(class(session), "BrowserSession"))) {
       session <- rtracklayer::browserSession()
     }
@@ -255,8 +254,9 @@ getIdeogram <- function(genome, subchr = NULL, cytobands = TRUE) {
     }
     if (cytobands) {
       message("Loading ideogram...")
+      GenomeInfoDb::genome(session) <- genome
       tryres <- try(query <-
-        rtracklayer::ucscTableQuery(session, "cytoBand", genome))
+        rtracklayer::ucscTableQuery(session, table = "cytoBand", genome = genome))
       if (!inherits(tryres, "try-error")) {
         rtracklayer::tableName(query) <- "cytoBand"
         df <- rtracklayer::getTable(query)
@@ -292,7 +292,7 @@ getIdeogram <- function(genome, subchr = NULL, cytobands = TRUE) {
     gr <- sort(gr)
     gr
   })
-  names(lst) <- .gnm
+  names(lst) <- genomes
   if (length(lst) == 1) {
     res <- lst[[1]]
   } else {