[BioC] Gviz question

[Hahne, Florian]

Hi Alex,
The missing rtracklayer import should be fixed now, please install the
latest Gviz version (0.99.2). Thanks for the hint. In the devel branch the
other packages and their name spaces are a bit of a moving target and it
is sometimes hard to keep up with changes...
For showing multiple chromosomes in one plot you would have to make use of
the 'add' argument of the plotTracks function, and create the necessary
trellis yourself. You'd have to use grid's viewport functionality, though.
Base graphics layout or mfcol/mfrow will not work here.
Here is a little dummy example:

chroms <- c("chr1", "chr2", "chr3", "chr4")
maTrack <- AnnotationTrack(range=GRanges(seqnames=chroms,
ranges=IRanges(start=1, width=c(100,400,200,1000)),
                                         strand=c("+", "+", "-", "+")),
genome="mm9", chromosome="chr1", name="foo")
mdTrack <- DataTrack(range=GRanges(seqnames=rep(chroms, c(10, 40, 20,
100)),             
ranges=IRanges(start=c(seq(1,100,len=10), seq(1,400,len=40), seq(1, 200,
len=20), 
                                                          seq(1,1000,
len=100)), width=9), values=runif(170)),
                     data="values", chromosome="chr1", genome="mm9",
name="bar")

mgTrack <- GenomeAxisTrack()
midTrack <- IdeogramTrack(genome="mm9", chromosome="chr1")
ncols <- 2
nrows <- length(chroms)%/%ncols
grid.newpage()
pushViewport(viewport(layout=grid.layout(nrows, ncols)))
for(i in seq_along(chroms)){
   pushViewport(viewport(layout.pos.col=((i-1)%%ncols)+1,
layout.pos.row=(((i)-1)%/%ncols)+1))
   plotTracks(list(midTrack, mgTrack, maTrack, mdTrack),
chromosome=chroms[i], add=TRUE)
   popViewport(1)
}


I added a section to the vignette explaining how to do this. It may become
useful at some point to add a high-level function that does all of this
automatically, but at this stage I think it is best to keep the package as
flexible as possible.

Florian


 



Florian Hahne
Novartis Institute For Biomedical Research
Translational Sciences / Preclinical Safety / PCS Informatics
Expert Data Integration and Modeling Bioinformatics
CHBS, WKL-135.2.26
Novartis Institute For Biomedical Research, Werk Klybeck
Klybeckstrasse 141
CH-4057 Basel
Switzerland
Phone: +41 61 6967127
Email : florian.hahne at novartis.com







On 3/6/12 4:56 AM, "Alexandre Kuhn" <alexandre.m.kuhn at gmail.com> wrote:

>Hello Florian,
>
>thank you for providing Gviz, a geat visualization tool that seems to
>nicely integrate with existing R objects (GenomicRanges, etc).
>
>I had to load rtracklayer separately for the ideogramTrack function to
>work. Is that expected? (see copy of my session below)
>
>Also, since a single chromosomes provides the genomic coordinates for
>all tracks in a plot, how could I use Gviz to display all chromosomes
>in a single plot (along with their respective AnnotationTrack for
>instance)?
>
>Best regards,
>Alex
>
>--
>R version 2.15.0 alpha (2012-03-03 r58572)
>Copyright (C) 2012 The R Foundation for Statistical Computing
>ISBN 3-900051-07-0
>Platform: x86_64-unknown-linux-gnu (64-bit)
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>
>> library("Gviz")
>Loading required package: grid
>> itrack <- IdeogramTrack(genome="hg19",chromosome="chr1")
>Error in eval(expr, envir, enclos) :
>  could not find function "ucscGenomes"
>> library("rtracklayer")
>Loading required package: GenomicRanges
>Loading required package: BiocGenerics
>
>Attaching package: ŒBiocGenerics¹
>
>The following object(s) are masked from Œpackage:stats¹:
>
>    xtabs
>
>The following object(s) are masked from Œpackage:base¹:
>
>    anyDuplicated, cbind, colnames, duplicated, eval, Filter, Find,
>    intersect, lapply, Map, mapply, order, paste, pmax, pmax.int, pmin,
>    pmin.int, Position, rbind, Reduce, rep.int, rownames, sapply,
>    setdiff, table, tapply, union, unique
>
>Loading required package: IRanges
>> itrack <- IdeogramTrack(genome="hg19",chromosome="chr1")
>> sessionInfo()
>R version 2.15.0 alpha (2012-03-03 r58572)
>Platform: x86_64-unknown-linux-gnu (64-bit)
>
>locale:
> [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
> [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
> [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
> [7] LC_PAPER=C                 LC_NAME=C
> [9] LC_ADDRESS=C               LC_TELEPHONE=C
>[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
>attached base packages:
>[1] grid      stats     graphics  grDevices utils     datasets  methods
>[8] base
>
>other attached packages:
>[1] rtracklayer_1.15.7   GenomicRanges_1.7.30 IRanges_1.13.28
>[4] BiocGenerics_0.1.11  Gviz_0.99.0
>
>loaded via a namespace (and not attached):
> [1] AnnotationDbi_1.17.23 Biobase_2.15.4        biomaRt_2.11.1
> [4] Biostrings_2.23.6     bitops_1.0-4.1        BSgenome_1.23.4
> [7] DBI_0.2-5             lattice_0.20-0        RColorBrewer_1.0-5
>[10] RCurl_1.91-1          Rsamtools_1.7.37      RSQLite_0.11.1
>[13] stats4_2.15.0         tools_2.15.0          XML_3.9-4
>[16] zlibbioc_1.1.1
>--