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

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.

Author
Jianhong Ou, Yong-Xu Wang, Lihua Julie Zhu
Date of publication
None
Maintainer
Jianhong Ou <jianhong.ou@umassmed.edu>
License
GPL (>= 2)
Version
1.10.2

View on Bioconductor

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
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
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"'
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"'

Files in this package

trackViewer/DESCRIPTION
trackViewer/NAMESPACE
trackViewer/NEWS
trackViewer/R
trackViewer/R/GRoperator.R
trackViewer/R/addArrowMark.R
trackViewer/R/addGuideLine.R
trackViewer/R/allclasses.R
trackViewer/R/coverageGR.R
trackViewer/R/dandelion.plot.R
trackViewer/R/geneModelFromTxdb.R
trackViewer/R/getHeight.R
trackViewer/R/grid.dandelion.R
trackViewer/R/grid.lollipop.R
trackViewer/R/importBam.R
trackViewer/R/importData.R
trackViewer/R/importScore.R
trackViewer/R/lollipop.plot.R
trackViewer/R/optimizeStyle.R
trackViewer/R/parse2GRanges.R
trackViewer/R/parseWIG.R
trackViewer/R/plotGRanges.R
trackViewer/R/plotGeneModel.R
trackViewer/R/plotLollipops.R
trackViewer/R/plotTrack.R
trackViewer/R/privateUtil.R
trackViewer/R/viewTracks.R
trackViewer/build
trackViewer/build/vignette.rds
trackViewer/inst
trackViewer/inst/doc
trackViewer/inst/doc/trackViewer.R
trackViewer/inst/doc/trackViewer.Rmd
trackViewer/inst/doc/trackViewer.html
trackViewer/inst/extdata
trackViewer/inst/extdata/cpsf160.repA_+.wig
trackViewer/inst/extdata/cpsf160.repA_-.wig
trackViewer/inst/extdata/cpsf160.repB_+.wig
trackViewer/inst/extdata/cpsf160.repB_-.wig
trackViewer/inst/extdata/fox2.bed
trackViewer/inst/extdata/map-pin-red.xml
trackViewer/inst/extdata/methy.bed
trackViewer/inst/unitTests
trackViewer/inst/unitTests/test_coverage.R
trackViewer/man
trackViewer/man/GRoperator.Rd
trackViewer/man/addArrowMark.Rd
trackViewer/man/addGuideLine.Rd
trackViewer/man/coverageGR.Rd
trackViewer/man/dandelion.plot.Rd
trackViewer/man/geneModelFromTxdb.Rd
trackViewer/man/getCurTrackViewport.Rd
trackViewer/man/importBam.Rd
trackViewer/man/importData.Rd
trackViewer/man/importScore.Rd
trackViewer/man/lolliplot.Rd
trackViewer/man/optimizeStyle.Rd
trackViewer/man/parse2GRanges.Rd
trackViewer/man/parseWIG.Rd
trackViewer/man/plotGRanges.Rd
trackViewer/man/pos.Rd
trackViewer/man/track.rd
trackViewer/man/trackList.Rd
trackViewer/man/trackStyle.Rd
trackViewer/man/trackViewer-package.Rd
trackViewer/man/trackViewerStyle.Rd
trackViewer/man/viewTracks.Rd
trackViewer/man/xscale.Rd
trackViewer/man/yaxisStyle.Rd
trackViewer/tests
trackViewer/tests/runTests.R
trackViewer/vignettes
trackViewer/vignettes/trackViewer.Rmd