Hi there,

I'm using rtracklayer's export function to get a bed file, and then I upload that file manually to the UCSC genome browser via my web browser. 

I am using the trackLine/colorByStrand function - it seems to be almost working fine, but not quite. It would be great if the colorByStrand option could put quotes around the color specifications.  Hopefully the code below shows the issue.

Thanks,

Janet

library(rtracklayer)
gr <- GRanges(seqnames="chr1", ranges=IRanges(start=c(1000,2000), width=100), strand=c("+","-") )
myColors <- cbind(col2rgb("red"),col2rgb("blue"))
myTrack <- new("BasicTrackLine", name="gr", description="gr", colorByStrand=myColors )
myTrack 
# track name=gr description=gr colorByStrand=255,0,0 0,0,255 
export(gr, "gr.bed", "BED", trackLine=myTrack )

### I get an error when I upload that to UCSC browser. Error looks like this:
# Error File 'gr.bed' - line 1 of custom input: variable needs to start with letter '0,0,255'

### the UCSC error goes away if I add quotes around the colors in the track line, like this
# track name=gr description=gr colorByStrand="255,0,0 0,0,255" 

sessionInfo()

R version 3.4.3 (2017-11-30)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.4

Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] rtracklayer_1.38.3   GenomicRanges_1.30.3 GenomeInfoDb_1.14.0  IRanges_2.12.0       S4Vectors_0.16.0     BiocGenerics_0.24.0 

loaded via a namespace (and not attached):
 [1] lattice_0.20-35            matrixStats_0.53.1         XML_3.98-1.10              Rsamtools_1.30.0          
 [5] Biostrings_2.46.0          GenomicAlignments_1.14.2   bitops_1.0-6               grid_3.4.3                
 [9] zlibbioc_1.24.0            XVector_0.18.0             Matrix_1.2-12              BiocParallel_1.12.0       
[13] tools_3.4.3                Biobase_2.38.0             RCurl_1.95-4.10            DelayedArray_0.4.1        
[17] compiler_3.4.3             SummarizedExperiment_1.8.1 GenomeInfoDbData_0.99.0   

Thanks, should be fixed in devel, 1.39.10. Btw, potential bugs are often better reported as a GitHub issue.

Thanks, Michael - appreciate it. Yes, I'll start using github instead for stuff like this.   

Maybe the github pages are worth a mention on http://www.bioconductor.org/help/support/posting-guide/  ?