trackViewer (version 1.8.3)

trackViewer-package: 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.

Details

ll{ 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.

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")