trackViewer-package: Minimal designed plotting tool for genomic data

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

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.

Author(s)

Maintainer: Jianhong Ou [e-mail] (ORCID)

Authors:

• Julie Lihua Zhu [e-mail]

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")

jianhong/trackViewer documentation built on Dec. 10, 2024, 10:33 a.m.