git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Gviz@69481 bc3139a8-67e5-0310-9ffc-ced21a209358
... | ... |
@@ -563,7 +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 |
+ genome(range) <- unname(genome) |
|
567 | 567 |
if(missing(chromosome) || is.null(chromosome)) |
568 | 568 |
chromosome <- if(length(range)>0) .chrName(as.character(seqnames(range)[1])) else "chrNA" |
569 | 569 |
## And finally the object instantiation, we have to distinguis between DetailsAnnotationTracks and normal ones |
... | ... |
@@ -746,7 +746,7 @@ GeneRegionTrack <- function(range=NULL, rstarts=NULL, rends=NULL, rwidths=NULL, |
746 | 746 |
if(is.null(end)) |
747 | 747 |
end <- if(!length(range)) NULL else max(IRanges::end(range)) |
748 | 748 |
genome <- if(missing(genome)) .getGenomeFromGRange(range, "NA") else genome |
749 |
- genome(range) <- genome |
|
749 |
+ genome(range) <- unname(genome) |
|
750 | 750 |
if(missing(chromosome) || is.null(chromosome)) |
751 | 751 |
chromosome <- if(length(range)>0) .chrName(as.character(seqnames(range)[1])) else "chrNA" |
752 | 752 |
new("GeneRegionTrack", start=start, end=end, chromosome=chromosome[1], range=range, |
... | ... |
@@ -851,7 +851,7 @@ setMethod("initialize", "BiomartGeneRegionTrack", function(.Object, start, end, |
851 | 851 |
gene=as.character(ens$gene_id), exon=as.character(ens$exon_id), |
852 | 852 |
transcript=as.character(ens$transcript_id), symbol=as.character(ens$symbol), |
853 | 853 |
rank=as.numeric(ens$rank)) |
854 |
- genome(range) <- list(...)$genome[1] |
|
854 |
+ genome(range) <- unname(list(...)$genome[1]) |
|
855 | 855 |
} |
856 | 856 |
if(length(range)==0) |
857 | 857 |
.Object <- setPar(.Object, "size", 0, interactive=FALSE) |
... | ... |
@@ -1321,7 +1321,7 @@ UcscTrack <- function(track, table=NULL, trackType=c("AnnotationTrack", "GeneReg |
1321 | 1321 |
if(missing(to)) |
1322 | 1322 |
to <- sessionInfo$chrInfo[chromosome] |
1323 | 1323 |
gr <- GRanges(ranges=IRanges(start=from, end=to), seqnames=chromosome) |
1324 |
- genome(gr) <- genome |
|
1324 |
+ genome(gr) <- unname(genome) |
|
1325 | 1325 |
query <- ucscTableQuery(sessionInfo$session, sessionInfo$track, gr) |
1326 | 1326 |
if(!is.null(table)) |
1327 | 1327 |
{ |