Minimal designed plotting tool for genomic data

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.

Author

Maintainer: Jianhong Ou jianhong.ou@duke.edu (ORCID)

Authors:

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")