Question

Gviz: Multiple BiomartGeneRegionTrack one object for Composite plots

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Entering edit mode

stephen.williams ▴ 10

@stephenwilliams-15198

Last seen 6.4 years ago

I'm trying to make a Composite plot of multiple gene regions. I've read the vignette, Chapter 6 on doing this. I'm able to plot my data but not the GeneRegionTrack using.

chroms <- c("chr2", "chr17")             
ncols <- 1
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(mdTrack),chromosome = chroms[i], type= "histogram", showId = TRUE, stacking = "dense", lty.grid="dashed", add = TRUE)
 popViewport(1)
}

Is there a way to have multiple genes regions stored in in a single object? Right now I'm using the BiomartGeneRegionTrack to pull my gene region data

geneTrack <-BiomartGeneRegionTrack(genome = "hg38",
              symbol = c("DNMT3A","RAI1"),
              cex = 2,
              fontsize = 15,
              stacking = "squish",
              name = "Ensembl Genes v92",
              background.title = "grey",
              biomart=biomaRt::useMart(biomart="ensembl", dataset="hsapiens_gene_ensembl"))

However, this only stores the last gene. In this case RAI1

Is it possible to plot two (or more) gene regions at the same time?

gviz gviz-package • 1.0k views

ADD COMMENT • link 6.5 years ago stephen.williams ▴ 10

0

Entering edit mode

For anyone interested I got this to work by ultimately plotting my tracks as per below. This method should be able to take any number of tracks and combine as many loci as you'd like.

grid.newpage()
pushViewport(viewport(layout = grid.layout(2,1)))

pushViewport(viewport(layout.pos.col = ((1 -1)%%1) + 1, layout.pos.row = (((1) -1)%/%1) + 1))
    plotTracks(list(rai1_gtrack, rai1_ht), type= "histogram", showId = TRUE, stacking = "dense", lty.grid="dashed", add = TRUE, fontsize = 13, title.width=1)
popViewport(1)

pushViewport(viewport(layout.pos.col = ((2 -1)%%1) + 1, layout.pos.row = (((2) -1)%/%1) + 1))
    plotTracks(list(dnmt3a_gtrack, dnmt3a_ht), type= "histogram", showId = TRUE, stacking = "dense", lty.grid="dashed", add = TRUE, reverseStrand=TRUE, fontsize = 13, title.width=1)
popViewport(1)

ADD REPLY • link 6.5 years ago stephen.williams ▴ 10