trackViewer-package {trackViewer} | R Documentation

## 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

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

        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 1.14.1 Index]