[BioC] Gviz - Beginner - Problem reproducing the provided examples

[Dan Tenenbaum]

On Thu, Sep 5, 2013 at 9:51 AM, Jager, Dominik <jager.9 at osu.edu> wrote:
> Hi,
>
> Sorry for the double post!
>
> I'm a R and Bioconductor beginner currently trying to get myself familiar with the Gviz package,
> thus "playing" around with the examples provided in the package manual. I'm using
> Bioconductor version 2.12 and this is what is happening:
>
>> library(GenomicRanges)
>> library(Gviz)
>> data(cpgIslands)
>> chr <- as.character(unique(seqnames(cpgIslands)))
>> gen <- genome(cpgIslands)
>> AnnotationTrack(cpgIslands, name = "CpG") -> atrack
>> GenomeAxisTrack() -> gtrack
>> plotTracks(atrack, gtrack)
>

I don't see this code in either the manual pages or the vignette of Gviz 1.4.5.
Furthermore, this code doesn't look right. Assignments go on the left,
 and use ",-", so  instead of

GenomeAxisTrack() -> gtrack

You want to say:

gtrack <- GenomeAxisTrack()

I suggest that you copy and paste the example you're interested in,
and then make one small change at a time until you get it to do what
you want.

Dan



> Fehler in rep(no, length.out = length(ans)) :
>   attempt to replicate an object of type 'S4'
>
> Further information:
>
> --------------------------------------------
>> traceback()
> 8: ifelse(is.null(from), -Inf, from)
> 7: ifelse(is.null(from), -Inf, from)
> 6: .local(x, ...)
> 5: FUN(X[[1L]], ...)
> 4: FUN(X[[1L]], ...)
> 3: lapply(trackList, subset, from = from, to = to, chromosome = chromosome,
>        sort = FALSE, stacks = FALSE, use.defaults = FALSE)
> 2: lapply(trackList, subset, from = from, to = to, chromosome = chromosome,
>        sort = FALSE, stacks = FALSE, use.defaults = FALSE)
> 1: plotTracks(atrack, gtrack)
>
> -----------------------------------------------------
>
>> sessionInfo()
> R version 3.0.1 (2013-05-16)
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> locale:
>  [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C               LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8
>  [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8    LC_PAPER=C                 LC_NAME=C
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] parallel  grid      stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] GenomicRanges_1.12.5 IRanges_1.18.3       BiocGenerics_0.6.0   Gviz_1.4.5           BiocInstaller_1.10.3
>
> loaded via a namespace (and not attached):
>  [1] AnnotationDbi_1.22.6   Biobase_2.20.1         biomaRt_2.16.0         Biostrings_2.28.0      biovizBase_1.8.1
>  [6] bitops_1.0-6           BSgenome_1.28.0        cluster_1.14.4         colorspace_1.2-2       DBI_0.2-7
> [11] dichromat_2.0-0        GenomicFeatures_1.12.3 Hmisc_3.12-2           labeling_0.2           lattice_0.20-23
> [16] munsell_0.4.2          plyr_1.8               RColorBrewer_1.0-5     RCurl_1.95-4.1         rpart_4.1-3
> [21] Rsamtools_1.12.4       RSQLite_0.11.4         rtracklayer_1.20.4     scales_0.2.3           stats4_3.0.1
> [26] stringr_0.6.2          tools_3.0.1            XML_3.98-1.1           zlibbioc_1.6.0
> ------------------------------------------------
>
> Thanks for you help!
>
> Dominik
>
>
> [The Ohio State University]
> Dr. Dominik Jäger
> Biological Sciences Department of Microbiology
> 405 Biological Science Building | 484 West 12th Avenue Columbus, OH 43210
> (614)-682-6890 Office
> jager.9 at osu.edu<mailto:jager.9 at osu.edu> osu.edu<http://osu.edu>
>
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>
>
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