[BioC] Gviz - Plot genes and data from - strand (3'-5') in 5'-3' direction

[Jager, Dominik]

...yes, thats correct.

So what I really want is to plot my data (see attached PNG) flipped by 180 degrees. So now the genes and the data were plotted in 3' to 5' direction, but I want in 5' to 3'/

Here some code:

> setwd("~/WORKING/")
> library(Gviz)
> options(ucscChromosomeNames = FALSE)
> tkgff <- import.gff3("~/WORKING/NC_006624.gff", format = "gff3", genome= "NC_06624.1", asRangedData = FALSE)
>atrack <- AnnotationTrack(tkgff, strand = "*", chromosome = chr, genome = gen, name = TK)
>gtrack <- GenomeAxisTrack()
> WIG <- import.wig("~/S0_20min_reverse.wig", asRangedData = FALSE)
> dtrack <- DataTrack(WIG, name = "S0+")
>from <- 1049512
> to <- 1052176
>plotTracks(list(gtrack,atrack, dtrack), from = from, to = to, cex = 1, type = "h")

I also attached the plot as PNG.


Dominik

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 osu.edu

________________________________________
Von: bioconductor-bounces at r-project.org [bioconductor-bounces at r-project.org]" im Auftrag von "Steve Lianoglou [lianoglou.steve at gene.com]
Gesendet: Donnerstag, 12. September 2013 09:57
An: Robert Ivanek
Cc: bioconductor at r-project.org list
Betreff: Re: [BioC] Gviz - Plot genes and data from - strand (3'-5') in 5'-3' direction

Hi,

On Thu, Sep 12, 2013 at 6:14 AM, Robert Ivanek <robert.ivanek at unibas.ch> wrote:
> Hi Dominik,
>
> You can achieve that by changing the strand in corresponding track
> objects.
[snip]

While this might change the strand of a gene, I do not think this is
what the OP is really after -- as I have previously been keen to try
to implement the approach that (I think) the OP wants.

I believe the OP would like to plot "the mirror image" of the plot
that Gviz would "normally" show given the start/stop coordinates that
the plotting functionality infers (or is given).

The approach you suggest wouldn't properly "flip" my gene models and
the data associated with them -- it would only show them on the
positive strand. The 5'utr of the gene that was originally on the
negative strand would look as if it were the 3'utr of the gene on the
(now annotated) positive strand, and vice versa, and if I were (say)
plotting ChIP-seq data over this locus, the TF would appear to be
binding the 3'utr of a gene on the positive strand (or downstream of
it), when that's not really the case.

-steve

--
Steve Lianoglou
Computational Biologist
Bioinformatics and Computational Biology
Genentech

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