% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/trackViewerPackage.R
\docType{package}
\name{trackViewer-package}
\alias{trackViewer}
\alias{trackViewer-package}
\title{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.
}
\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")
}
\author{
\strong{Maintainer}: Jianhong Ou \email{jianhong.ou@duke.edu} (\href{https://orcid.org/0000-0002-8652-2488}{ORCID})

Authors:
\itemize{
  \item Julie Lihua Zhu \email{Julie.Zhu@umassmed.edu}
}

}
