[BioC] ggbio : misplaced tracks in a test case

[Abhishek Pratap]

I am trying to run a test case in ggbio(based on example in a vignette) and
seem to be running into an odd case where a feature is misplaced on the
graph. working Example below

In the plot I see the variation(rectangle) is misplaced. I see it on chr3
whereas it should be on chr1. plot also attached


library(ggbio)
data(hg19Ideogram, package = "biovizBase")
## subset_chr
chr.sub <- paste("chr", 1:3, sep = "")
new.names <- as.character(1:3)
names(new.names) <- paste("chr",new.names,sep="")
hg19Ideo <- hg19Ideogram
hg19Ideo <- keepSeqlevels(hg19Ideogram,chr.sub)
hg19Ideo <- renameSeqlevels(hg19Ideo,new.names)


p <- ggplot() +
layout_circle(hg19Ideo,geom="ideo",fill="gray70",radius=30,trackWidth=4)
#adding the scale track
p <- p +
layout_circle(hg19Ideo,geom="scale",fill="gray70",size=4,radius=35,trackWidth=2)
#adding the text track
p <- p +
layout_circle(hg19Ideo,geom="text",aes(label=seqnames),vjust=0,radius=39,trackWidth=7,size=6)


#testing : placing a rect for a dummy variation
test_gr <- GRanges('1',IRanges(start=3000,width=1))

#adding the mutant track
p <- p +
layout_circle(test_gr,geom="rect",color="steelblue",radius=23,trackWidth=6)
p




Thanks!
-Abhi




> sessionInfo()R version 2.15.2 (2012-10-26)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
LC_TIME=en_US.UTF-8
 [4] LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8
LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=C                 LC_NAME=C
LC_ADDRESS=C
[10] LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8
LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] biovizBase_1.6.2     rtracklayer_1.18.2   ggbio_1.6.4
ggplot2_0.9.3
[5] GenomicRanges_1.10.5 IRanges_1.16.3       BiocGenerics_0.4.0
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