trackViewer-package {trackViewer} | R Documentation

## Minimal designed plotting tool for genomic data

### Description

A package that plot data and annotation information along genomic coordinates in an elegance style. This tool is based on Gviz but want to draw figures in minimal style for publication.

### Author(s)

Maintainer: Jianhong Ou jianhong.ou@duke.edu (ORCID)

Authors:

- Julie Lihua Zhu Julie.Zhu@umassmed.edu

### Examples

    library(TxDb.Hsapiens.UCSC.hg19.knownGene)
    library(org.Hs.eg.db)
    trs <- geneModelFromTxdb(TxDb.Hsapiens.UCSC.hg19.knownGene,
                             org.Hs.eg.db,
                             chrom="chr11",
                             start=122929275,
                             end=122930122)
    extdata <- system.file("extdata", package="trackViewer",
                           mustWork=TRUE)
    repA <- importScore(paste(extdata, "cpsf160.repA_+.wig", sep="/"),
                        paste(extdata, "cpsf160.repA_-.wig", sep="/"),
                        format="WIG")
    strand(repA@dat) <- "+"
    strand(repA@dat2) <- "-"
    fox2 <- importScore(paste(extdata, "fox2.bed", sep="/"), format="BED")
    dat <- coverageGR(fox2@dat)
    fox2@dat <- dat[strand(dat)=="+"]
    fox2@dat2 <- dat[strand(dat)=="-"]
    gr <- GRanges("chr11", IRanges(122929275, 122930122), strand="-")
    vp <- viewTracks(trackList(repA, fox2, trs), gr=gr, autoOptimizeStyle=TRUE)
    addGuideLine(c(122929767, 122929969), vp=vp)
    addArrowMark(list(x=unit(.5, "npc"),
                      y=unit(.39, "npc")),
                 col="blue")

[Package trackViewer version 1.24.2 Index]