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

[Robert Ivanek]

I see, sorry I got it wrong.
It cannot be done automatically in Gviz but maybe following can help you:

library(GenomicRanges)
library(Gviz)

genes.gr <- GRanges("chr1", IRanges(c(10,20,30,40), width=8),
                    strand=c("+","-","+","-"))
aT <- AnnotationTrack(genes.gr)

reads.gr <- GRanges("chr1", IRanges(seq(1,50,2), width=1),
                    strand="+", count=seq(1,50,2))
dT1 <- DataTrack(reads.gr)

## this function expects DataTrack in which you would like to flip the
points and AnnotationTrack with genes which would define regions you
would like to flip, those regions (genes) have to be on minus strand

reverseCounts <- function(reads, genes) {
    genes <- genes[strand(genes)=="-"]
    strand(genes) <- "*"
    ##
    ov <- findOverlaps(ranges(reads), ranges(genes))
    indx <- split(queryHits(ov), subjectHits(ov))
    indx <- lapply(indx, rev)
    indx <- unlist(indx)
    values(reads)[,queryHits(ov)] <- values(reads)[,indx]
    ##
    return(reads)
}
##
dT2 <- reverseCounts(dT1, aT)
##
plotTracks(list(aT, dT1, dT2))

Is that what you want?
Best
Robert


On 12/09/13 16:21, Jager, Dominik wrote:
> ...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
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
> 
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>