git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Gviz@69407 bc3139a8-67e5-0310-9ffc-ced21a209358
... | ... |
@@ -563,6 +563,7 @@ AnnotationTrack <- function(range=NULL, start=NULL, end=NULL, width=NULL, featur |
563 | 563 |
defaults=list(feature="unknown", group=group, id=id, strand=strand, density=1), |
564 | 564 |
chromosome=chromosome) |
565 | 565 |
genome <- if(missing(genome)) .getGenomeFromGRange(range, "NA") else genome |
566 |
+ genome(range) <- genome |
|
566 | 567 |
if(missing(chromosome) || is.null(chromosome)) |
567 | 568 |
chromosome <- if(length(range)>0) .chrName(as.character(seqnames(range)[1])) else "chrNA" |
568 | 569 |
## And finally the object instantiation, we have to distinguis between DetailsAnnotationTracks and normal ones |
... | ... |
@@ -745,6 +746,7 @@ GeneRegionTrack <- function(range=NULL, rstarts=NULL, rends=NULL, rwidths=NULL, |
745 | 746 |
if(is.null(end)) |
746 | 747 |
end <- if(!length(range)) NULL else max(IRanges::end(range)) |
747 | 748 |
genome <- if(missing(genome)) .getGenomeFromGRange(range, "NA") else genome |
749 |
+ genome(range) <- genome |
|
748 | 750 |
if(missing(chromosome) || is.null(chromosome)) |
749 | 751 |
chromosome <- if(length(range)>0) .chrName(as.character(seqnames(range)[1])) else "chrNA" |
750 | 752 |
new("GeneRegionTrack", start=start, end=end, chromosome=chromosome[1], range=range, |
... | ... |
@@ -849,6 +851,7 @@ setMethod("initialize", "BiomartGeneRegionTrack", function(.Object, start, end, |
849 | 851 |
gene=as.character(ens$gene_id), exon=as.character(ens$exon_id), |
850 | 852 |
transcript=as.character(ens$transcript_id), symbol=as.character(ens$symbol), |
851 | 853 |
rank=as.numeric(ens$rank)) |
854 |
+ genome(range) <- list(...)$genome[1] |
|
852 | 855 |
} |
853 | 856 |
if(length(range)==0) |
854 | 857 |
.Object <- setPar(.Object, "size", 0, interactive=FALSE) |