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

[Robert Ivanek]

Hi Dominik,

You can achieve that by changing the strand in corresponding track
objects. You did not provide any code so I can only suggest a solution
based on example from vignette:

library(Gviz)
from <- 65921878
to <- 65980988
knownGenes <- UcscTrack(genome = "mm9", chromosome = "chrX",
                        track = "knownGene", from = from, to = to,
                        trackType = "GeneRegionTrack",
                        rstarts = "exonStarts", rends = "exonEnds",
                        gene = "name", symbol = "name",
                        transcript = "name", strand = "strand",
                        fill = "#8282d2", name = "UCSC Genes")

## by running ploTracks now you can see that some gene(s)
## are on minus strand
plotTracks(knownGenes)

## change the strand of knowGenes (which is UcscTrack object)
strand(knownGenes) <- "+"

## by calling the plotTracks again you can see all genes
## are now on plus strand
plotTracks(knownGenes)


Best
Robert

On 12/09/13 13:30, Jager, Dominik wrote:
> Hi,
> 
> I'm using the Gviz package to visualize some RNA-seq data. Everything works great so far, however
> I was wondering if there is a simple way to display genes (and corresponding datatracks) which are encoded on the - strand of the genome on the + strand? I really would like to plot a certain set of genes all in 5'-> 3' direction independently on which strand they are encoded...
> 
> 
> Thanks for your 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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