trackViewer-package {trackViewer} | R Documentation |
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.
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.
Jianhong Ou, Julie Lihua Zhu
Maintainer: Jianhong Ou <jianhong.ou@umassmed.edu>
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")