trackViewer: A bioconductor package with minimalist design for drawing elegant tracks or lollipop plot
Version 1.12.0

Visualize mapped reads along with annotation as track layers for NGS dataset such as ChIP-seq, RNA-seq, miRNA-seq, DNA-seq, SNPs and methylation data.

Browse man pages Browse package API and functions Browse package files

AuthorJianhong Ou, Yong-Xu Wang, Lihua Julie Zhu
Bioconductor views Visualization
Date of publicationNone
MaintainerJianhong Ou <jianhong.ou@umassmed.edu>
LicenseGPL (>= 2)
Version1.12.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("trackViewer")

Man pages

addArrowMark: Add arrow mark to the figure at a given position
addGuideLine: Add guide lines to the tracks
coverageGR: calculate coverage
dandelion.plot: dandelion.plots
geneModelFromTxdb: Prepare gene model from an object of TxDb
getCurTrackViewport: Get current track viewport
GRoperator: GRanges operator
ideogramPlot: plot ideogram with data
importBam: Reading data from a BAM file
importData: Reading data from a BED or WIG file to RleList
importScore: Reading data from a BED or WIG file
loadIdeogram: load ideogram from UCSC
lolliplot: Lolliplots
optimizeStyle: Optimize the style of plot
parse2GRanges: parse text into GRanges
parseWIG: convert WIG format track to BED format track
plotGRanges: plot GRanges data
pos: Class '"pos"'
track: Class '"track"'
trackList: List of tracks
trackStyle: Class '"trackStyle"'
trackViewer-package: Minimal designed plotting tool for genomic data
trackViewerStyle: Class '"trackViewerStyle"'
viewTracks: plot the tracks
xscale: Class '"xscale"'
yaxisStyle: Class '"yaxisStyle"'

Functions

$,track-method Man page
$<-,track-method Man page
GRbin Source code
GRoperator Man page Source code
Y1pos Source code
addArrowMark Man page Source code
addGuideLine Man page Source code
condenceGRs Source code
convertFont Source code
convertHeight2NPCnum Source code
coverageGR Man page Source code
dandelion.plot Man page Source code
disjoinGRs Source code
drawXaxis Source code
drawXscale Source code
drawYaxis Source code
filterTracks Source code
geneModelFromTxdb Man page Source code
getColNum Source code
getCurTrackViewport Man page Source code
getHeight Source code
getYheight Source code
getYlim Source code
gieStain Source code
grid.dan Source code
grid.dandelion Source code
grid.lollipop Source code
grid.pie Source code
gridPlot Source code
hrScale Source code
ideogramPlot Man page Source code
importBam Man page Source code
importData Man page Source code
importScore Man page Source code
jitterLables Source code
loadIdeogram Man page Source code
locateScale Source code
lolliplot Man page Source code
maxStringWidth Source code
optFontSize Source code
optFontSize1 Source code
optimizeStyle Man page Source code
orderedGR Source code
parse2GRanges Man page Source code
parseWIG Man page Source code
plotDataTrack Source code
plotFeatures Source code
plotGRanges Man page Source code
plotGeneModel Source code
plotIdeo Source code
plotLegend Source code
plotLollipops Source code
plotOneIdeo Source code
plotTrack Source code
pos Man page
pos-class Man page
putGeneYlab Source code
putYlab Source code
reAdjustLabels Source code
rgb2hex Source code
setTrackStyleParam Man page
setTrackStyleParam,track,character,ANY-method Man page
setTrackStyleParam,track,character-method Man page
setTrackViewerStyleParam Man page
setTrackViewerStyleParam,trackViewerStyle,character,ANY-method Man page
setTrackViewerStyleParam,trackViewerStyle,character-method Man page
setTrackXscaleParam Man page
setTrackXscaleParam,track,character,ANY-method Man page
setTrackXscaleParam,track,character-method Man page
setTrackYaxisParam Man page
setTrackYaxisParam,track,character,ANY-method Man page
setTrackYaxisParam,track,character-method Man page
show,track-method Man page
track Man page
track-class Man page
trackList Man page Source code
trackList-class Man page
trackStyle Man page
trackStyle-class Man page
trackViewer Man page
trackViewer-package Man page
trackViewerStyle Man page Source code
trackViewerStyle-class Man page
viewTracks Man page Source code
xscale Man page
xscale-class Man page
yaxisStyle Man page
yaxisStyle-class Man page

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/GRoperator.R
R/addArrowMark.R
R/addGuideLine.R
R/allclasses.R
R/coverageGR.R
R/dandelion.plot.R
R/geneModelFromTxdb.R
R/getHeight.R
R/grid.dandelion.R
R/grid.lollipop.R
R/ideogramPlot.R
R/importBam.R
R/importData.R
R/importScore.R
R/loadIdeogram.R
R/lollipop.plot.R
R/optimizeStyle.R
R/parse2GRanges.R
R/parseWIG.R
R/plotGRanges.R
R/plotGeneModel.R
R/plotIdeo.R
R/plotLollipops.R
R/plotOneIdeo.R
R/plotTrack.R
R/privateUtil.R
R/viewTracks.R
build
build/vignette.rds
inst
inst/doc
inst/doc/trackViewer.R
inst/doc/trackViewer.Rmd
inst/doc/trackViewer.html
inst/extdata
inst/extdata/cpsf160.repA_+.wig
inst/extdata/cpsf160.repA_-.wig
inst/extdata/cpsf160.repB_+.wig
inst/extdata/cpsf160.repB_-.wig
inst/extdata/fox2.bed
inst/extdata/ideo.hg38.rds
inst/extdata/map-pin-red.xml
inst/extdata/methy.bed
inst/unitTests
inst/unitTests/test_coverage.R
man
man/GRoperator.Rd
man/addArrowMark.Rd
man/addGuideLine.Rd
man/coverageGR.Rd
man/dandelion.plot.Rd
man/geneModelFromTxdb.Rd
man/getCurTrackViewport.Rd
man/ideogramPlot.Rd
man/importBam.Rd
man/importData.Rd
man/importScore.Rd
man/loadIdeogram.Rd
man/lolliplot.Rd
man/optimizeStyle.Rd
man/parse2GRanges.Rd
man/parseWIG.Rd
man/plotGRanges.Rd
man/pos.Rd
man/track.rd
man/trackList.Rd
man/trackStyle.Rd
man/trackViewer-package.Rd
man/trackViewerStyle.Rd
man/viewTracks.Rd
man/xscale.Rd
man/yaxisStyle.Rd
tests
tests/runTests.R
vignettes
vignettes/trackViewer.Rmd
trackViewer documentation built on May 20, 2017, 10:49 p.m.