Dandelion Plot | Change the type of Dandelion plot | Change the number of dandelions | Add y-axis (yaxis) | Session Info
Package: trackViewer 1.49.0
Jianhong Ou
trackViewer: A R/Bioconductor package with web interface for drawing elegant interactive tracks or lollipop plot to facilitate integrated analysis of multi-omics data
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.
Authors:
trackViewer_1.49.0.tar.gz
trackViewer_1.49.0.zip(r-4.7)trackViewer_1.49.0.zip(r-4.6)trackViewer_1.49.0.zip(r-4.5)
trackViewer_1.49.0.tgz(r-4.6-any)trackViewer_1.49.0.tgz(r-4.5-any)
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trackViewer_1.49.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
trackViewer/json (API)
| # Install 'trackViewer' in R: |
| install.packages('trackViewer', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
On BioConductor:trackViewer-1.49.0(bioc 3.24)trackViewer-1.48.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated from:ea7da89d27. Checks:1 WARNING, 9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 309 | ||
| linux-devel-x86_64 | OK | 625 | ||
| source / vignettes | OK | 863 | ||
| linux-release-x86_64 | OK | 621 | ||
| macos-release-arm64 | OK | 345 | ||
| macos-oldrel-arm64 | OK | 335 | ||
| windows-devel | OK | 539 | ||
| windows-release | OK | 524 | ||
| windows-oldrel | OK | 525 | ||
| wasm-release | OK | 282 |
Exports:addArrowMarkaddGuideLineaddInteractionAnnotationARAbrowseTracksbrowseTracksOutputcoverageGRdandelion.plotgeneModelFromTxdbgeneTrackgetCurTrackViewportgetGeneIDsFromTxDbgetLocationgi2trackgieStainGIoperatorGRoperatorideogramPlotimportBamimportDataimportGInteractionsimportScorelistChromosomeslistNormalizationslistResolutionsloadIdeogramlolliplotoptimizeStyleparse2GRangesparseWIGplotGRangesreducerenderbrowseTracksseqlevelsseqlevelsStyleseqlevelsStyle<-setTrackStyleParamsetTrackViewerStyleParamsetTrackXscaleParamsetTrackYaxisParamshowtrackListtrackViewerStyleviewGeneviewTracks
Dependencies:abindAnnotationDbiAnnotationFilteraskpassbackportsbase64encBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocIObiocmakeBiocParallelbiomaRtBiostringsbiovizBasebitbit64bitopsblobBSgenomebslibcachemcheckmatecigarillocliclustercodetoolscolorspacecpp11crayoncurldata.tableDBIdbplyrDelayedArraydeldirdichromatdigestdir.expirydplyrensembldbevaluatefarverfastmapfilelockfontawesomeforeignformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2gluegridExtragrImportgtableGvizhighrHmischmshtmlTablehtmltoolshtmlwidgetshttrhttr2InteractionSetinterpIRangesisobandjpegjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlatticelatticeExtralazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemimennetopensslpillarpkgconfigpngprettyunitsprogressProtGenericspurrrR6rappdirsRColorBrewerRcppRcppEigenRCurlrestfulrrhdf5rhdf5filtersRhdf5libRhtslibrjsonrlangrmarkdownrpartRsamtoolsRSQLiterstudioapirtracklayerS4ArraysS4VectorsS7sassscalesSeqinfosnowSparseArraystrawrstringistringrSummarizedExperimentsystibbletidyrtidyselecttinytextxdbmakerUCSC.utilsutf8VariantAnnotationvctrsviridisLitewithrxfunXMLxml2XVectoryaml
trackViewer Vignette: dandelionPlot
Last update: 2026-03-18
Started: 2021-04-01
trackViewer Vignette: change the track styles
Prepare toy data | Using the browseTracks function as a helper | Adjust the x-axis or the X scale | Adjust the y-axis | Adjust the label of y-axis | Adjust the track color | Adjust the track height | Change the track names | Show paired data in the same track | Show signals and the called peaks | Flip the x-axis | Optimize the theme | Plot with breaks | Session Info
Last update: 2024-12-03
Started: 2021-04-01
trackViewer Vignette: plot interaction data
Introduction | Plot chromatin interactions data in linear layout | Session Info
Last update: 2024-11-08
Started: 2021-04-01
trackViewer Vignette: lollipopPlot
Lolliplot | Change the lolliplot color | Change the color of the features. | Change the color and opacity of the lollipop. | Add the index labels in the node | Change the height of the features | Plot multiple transcripts in the features | Change the height of a lollipop plot | Customize the x-axis label position | Customize the y-axis label position | Jitter the label | Add a legend | Control the labels | Change the lolliplot type | Change the shape for "circle" plot | Google pin | Flag | Pie plot | Plot multiple samples | Multiple layers | pie.stack layout | Caterpillar layout | EMBL-EBI Proteins API | Variant Call Format (VCF) data | Methylation data | Change the node size | Change the scale of the x-axis (xscale) | Split the lollipop plot into multiLayers | Plot the lollipop plot with the coverage and annotation tracks | Session Info
Last update: 2024-09-05
Started: 2021-04-01
trackViewer Vignette: overview
Introduction | Browse | Steps of using trackViewer \Biocpkg | Step 1. Import data | Step 2. Build the gene model | Step 3. View the tracks | Generate and edit an interactive plot using the browseTracks function | Plot multiple genes in one track | Operators | Lolliplot | Dandelion Plot | Plot chromatin interactions data | Ideogram Plot | Web application of trackViewer | Session Info
Last update: 2024-02-08
Started: 2015-10-02
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Minimal designed plotting tool for genomic data | trackViewer-package trackViewer |
| Add arrow mark to the figure at a given position | addArrowMark |
| Add guide lines to the tracks | addGuideLine |
| Add annotation markers to the figure at a given position | addInteractionAnnotation |
| Aggregate Region Analysis | ARA |
| browse tracks | browseTracks |
| Shiny bindings for browseTracks | browseTracks-shiny browseTracksOutput renderbrowseTracks |
| calculate coverage | coverageGR |
| dandelion.plots | dandelion.plot |
| Prepare gene model from an object of TxDb | geneModelFromTxdb |
| track from TxDb | geneTrack |
| Get current track viewport | getCurTrackViewport |
| get gene ids by genomic location | getGeneIDsFromTxDb |
| get genomic location by gene symbol | getLocation |
| convert GInteractions to track object | gi2track |
| color sheme for the schema for Chromosome Band (Ideogram) | gieStain |
| GInteractions operator | GIoperator |
| plot GRanges metadata | gridPlot |
| GRanges operator | GRoperator |
| plot ideogram with data | ideogramPlot |
| Reading data from a BAM file | importBam |
| Reading data from a BED or WIG file to RleList | importData |
| Reading data from a ginteractions, hic, cool, or validPairs file | importGInteractions |
| Reading data from a BED or WIG file | importScore |
| plot tracks for single cell RNAseq | importScSeqScore |
| List the available chromosome | listChromosomes |
| List the available normalizations | listNormalizations |
| List the available resolutions | listResolutions |
| load ideogram from UCSC | loadIdeogram |
| Lolliplots | lolliplot |
| Optimize the style of plot | optimizeStyle |
| parse text into GRanges | parse2GRanges |
| convert WIG format track to BED format track | parseWIG |
| plot GRanges data | plotGRanges |
| plot ideogram | plotIdeo |
| plot ideogram with data for one chromosome | plotOneIdeo |
| Class '"pos"' | pos pos-class |
| Reduce method for 'GInteractions' | reduce,GInteractions reduce,GInteractions-method |
| List of tracks | seqlevelsStyle<-,trackList-method trackList trackList-class |
| Class '"trackStyle"' | $,track-method $,trackStyle-method $<-,track-method $<-,trackStyle-method seqlevels,track-method seqlevelsStyle,track-method seqlevelsStyle<-,track-method setTrackStyleParam setTrackStyleParam,track,character,ANY-method setTrackStyleParam,track,character-method setTrackXscaleParam setTrackXscaleParam,track,character,ANY-method setTrackXscaleParam,track,character-method setTrackYaxisParam setTrackYaxisParam,track,character,ANY-method setTrackYaxisParam,track,character-method show,track-method track track-class trackStyle trackStyle-class |
| Class '"trackViewerStyle"' | setTrackViewerStyleParam setTrackViewerStyleParam,trackViewerStyle,character,ANY-method setTrackViewerStyleParam,trackViewerStyle,character-method trackViewerStyle trackViewerStyle-class |
| plot tracks based on gene name | viewGene |
| plot the tracks | viewTracks |
| Class '"xscale"' | xscale xscale-class |
| Class '"yaxisStyle"' | yaxisStyle yaxisStyle-class |