Minimal designed plotting tool for genomic data

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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.

Details

Package: trackViewer
Type: Package
Version: 1.0
Date: 2013-10-18
License: Artistic-2.0

This package is minimal designed to plot figure for publication.

Author(s)

Jianhong Ou, Julie Lihua Zhu

Maintainer: Jianhong Ou <jianhong.ou@umassmed.edu>

Examples

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    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")