A R/Bioconductor package for drawing elegant interactive tracks or lollipop plot to facilitate integrated analysis of multi-omics 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

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

    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")