R/trackViewerPackage.R

In trackViewer: A R/Bioconductor package with web interface for drawing elegant interactive tracks or lollipop plot to facilitate integrated analysis of multi-omics data

#' @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")
"_PACKAGE"