Thanks for reporting the issue, it's clearly another bug, I will work on
that today!

cheers

Tengfei


On Mon, Nov 25, 2013 at 2:20 PM, Leonardo Collado Torres <lcollado@jhsph.edu
> wrote:

> Hello Tengfei and BioC list,
>
> I believe that tracks() and plotIdeogram() are not working as intended in
> ggbio 1.10.9 Page 20 of
> http://www.bioconductor.org/packages/release/bioc/vignettes/ggbio/inst/doc/ggbio.pdf shows
> a tracks example plot with an ideogram. I think that tracks() is not
> handling properly the ggplot2 controls for the ideogram track as it is
> adding what looks like a layer label ("chr1" in grey) and a discrete scale
> (probably scale_fill_discrete) for the cytobands.
>
> You can produce the plot using the code in pages 19 and 20 from the
> vignette (pasted below):
>
> > library(ggbio)
> > ## require internet connection
> > p.ideo <- plotIdeogram(genome = "hg19")
> Loading...
> Done
> use chr1 automatically
> > library(TxDb.Hsapiens.UCSC.hg19.knownGene)
> > txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
> > wh <- GRanges("chr16", IRanges(30064491, 30081734))
> > p1 <- autoplot(txdb, which = wh, names.expr = "gene_id")
> Aggregating TranscriptDb...
> Parsing exons...
> Parsing cds...
> Parsing transcripts...
> Parsing utrs...
> ------exons...
> ------cdss...
> ------introns...
> ------utr...
> aggregating...
> Done
> Constructing graphics...
> Warning message:
> In ans[] <- x :
>   number of items to replace is not a multiple of replacement length
> > p2 <- autoplot(txdb, which = wh, stat = "reduce", color = "brown",
> + fill = "brown")
> Aggregating TranscriptDb...
> Parsing exons...
> Parsing cds...
> Parsing transcripts...
> Parsing utrs...
> ------exons...
> ------cdss...
> ------introns...
> ------utr...
> aggregating...
> Done
> Constructing graphics...
> Warning message:
> In ans[] <- x :
>   number of items to replace is not a multiple of replacement length
> > tracks(p.ideo, full = p1, reduce = p2, heights = c(1.5, 5, 1)) +
> + ylab("") + theme_tracks_sunset()
>
> I noticed this when using:
>
>  > library(derfinder) ## From https://github.com/lcolladotor/derfinder
> > example("plotCluster", "derfinder")
>
>
> Session info:
>
> > sessionInfo()
> R version 3.0.2 (2013-09-25)
> Platform: x86_64-apple-darwin10.8.0 (64-bit)
>
> 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  stats     graphics  grDevices utils     datasets  methods
> base
>
> other attached packages:
>  [1] bumphunter_1.3.3                         locfit_1.5-9.1
>             iterators_1.0.6
>  [4] foreach_1.4.1                            derfinder_0.0.37
>             RcppArmadillo_0.3.920.3
>  [7] Rcpp_0.10.6
>  TxDb.Hsapiens.UCSC.hg19.knownGene_2.10.1 GenomicFeatures_1.14.2
>
> [10] AnnotationDbi_1.24.0                     Biobase_2.22.0
>             rtracklayer_1.22.0
> [13] GenomicRanges_1.14.3                     XVector_0.2.0
>              IRanges_1.20.6
> [16] BiocGenerics_0.8.0                       ggbio_1.10.9
>             ggplot2_0.9.3.1
>
> loaded via a namespace (and not attached):
>  [1] biomaRt_2.18.0          Biostrings_2.30.1       biovizBase_1.10.4
>   bitops_1.0-6            BSgenome_1.30.0
>  [6] cluster_1.14.4          codetools_0.2-8         colorspace_1.2-4
>    DBI_0.2-7               dichromat_2.0-0
> [11] digest_0.6.3            doRNG_1.5.5             Formula_1.1-1
>   grid_3.0.2              gridExtra_0.9.1
> [16] gtable_0.1.2            Hmisc_3.13-0            itertools_0.1-1
>   labeling_0.2            lattice_0.20-24
> [21] MASS_7.3-29             matrixStats_0.8.12      munsell_0.4.2
>   pkgmaker_0.17.4         plyr_1.8
> [26] proto_0.3-10            qvalue_1.36.0           R.methodsS3_1.5.2
>   RColorBrewer_1.0-5      RCurl_1.95-4.1
> [31] registry_0.2            reshape2_1.2.2          rngtools_1.2.3
>    Rsamtools_1.14.2        RSQLite_0.11.4
> [36] scales_0.2.3            splines_3.0.2           stats4_3.0.2
>    stringr_0.6.2           survival_2.37-4
> [41] tcltk_3.0.2             tools_3.0.2
> VariantAnnotation_1.8.6 XML_3.95-0.2            xtable_1.7-1
> [46] zlibbioc_1.8.0
>
>
> Best,
> Leonardo
>
> Leonardo Collado Torres, PhD student
> Department of Biostatistics
> Johns Hopkins University
> Bloomberg School of Public Health
> Website: http://www.biostat.jhsph.edu/~lcollado/<http://bit.ly/LColladoTorres>
> Blog: http://lcolladotor.github.io/ <http://bit.ly/FellBit>
>
>
>
>


-- 
Tengfei Yin, PhD
Seven Bridges Genomics
sbgenomics.com
625 Mt. Auburn St. Suite #208
Cambridge, MA 02138
(617) 866-0446

	[[alternative HTML version deleted]]

