Introduction | Tutorial and Examples | Quick Start | Creating a karyotype plot | Genomes and Chromosomes | Types of Plots | Adding Axis | Changing the plotting parameters | Zooming: plotting small parts of the genome | Clipping and cutting the object representation | Adding Data | Common Parameters | Basic Plotting Functions | Higher Level Plotting Functions | Compatibility with r BiocStyle::Biocpkg("magrittr") | Session Info
Package: karyoploteR 1.39.0
Bernat Gel
karyoploteR: Plot customizable linear genomes displaying arbitrary data
karyoploteR creates karyotype plots of arbitrary genomes and offers a complete set of functions to plot arbitrary data on them. It mimicks many R base graphics functions coupling them with a coordinate change function automatically mapping the chromosome and data coordinates into the plot coordinates. In addition to the provided data plotting functions, it is easy to add new ones.
Authors:
karyoploteR_1.39.0.tar.gz
karyoploteR_1.39.0.zip(r-4.7)karyoploteR_1.39.0.zip(r-4.6)karyoploteR_1.39.0.zip(r-4.5)
karyoploteR_1.39.0.tgz(r-4.6-any)karyoploteR_1.39.0.tgz(r-4.5-any)
karyoploteR_1.39.0.tar.gz(r-4.7-any)karyoploteR_1.39.0.tar.gz(r-4.6-any)
karyoploteR_1.39.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
karyoploteR/json (API)
| # Install 'karyoploteR' in R: |
| install.packages('karyoploteR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/bernatgel/karyoploter/issues
On BioConductor:karyoploteR-1.39.0(bioc 3.24)karyoploteR-1.38.0(bioc 3.23)
visualizationcopynumbervariationsequencingcoveragednaseqchipseqmethylseqdataimportonechannelbioconductorbioinformaticsdata-visualizationgenomegenomics-visualizationplotting-in-r
Last updated from:3e8c8b101b. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 385 | ||
| linux-devel-x86_64 | NOTE | 814 | ||
| source / vignettes | OK | 525 | ||
| linux-release-x86_64 | NOTE | 779 | ||
| macos-release-arm64 | NOTE | 716 | ||
| macos-oldrel-arm64 | NOTE | 660 | ||
| windows-devel | NOTE | 724 | ||
| windows-release | NOTE | 681 | ||
| windows-oldrel | NOTE | 699 | ||
| wasm-release | OK | 312 |
Exports:addGeneNamesautotrackcolByCategorycolByChrcolByRegioncolByValuedarkerfilterParamsfindIntersectionsgetChromosomeNamesBoundingBoxgetColorSchemasgetCytobandColorsgetCytobandsgetDataPanelBoundingBoxgetDefaultPlotParamsgetMainTitleBoundingBoxgetTextSizegetVariantsColorshorizonColorsis.colorkpAblinekpAddBaseNumberskpAddChromosomeNameskpAddChromosomeSeparatorskpAddColorRectkpAddCytobandLabelskpAddCytobandskpAddCytobandsAsLinekpAddLabelskpAddMainTitlekpAreakpArrowskpAxiskpBarskpDataBackgroundkpHeatmapkpLineskpPlotBAMCoveragekpPlotBAMDensitykpPlotBigWigkpPlotCoveragekpPlotDensitykpPlotGeneskpPlotHorizonkpPlotLinkskpPlotLoesskpPlotManhattankpPlotMarkerskpPlotNameskpPlotRainfallkpPlotRegionskpPlotRibbonkpPlotTranscriptskpPointskpPolygonkpRectkpSegmentskpTextlightermakeGenesDataFromTxDbmergeTranscriptsplotDefaultPlotParamsplotKaryotypeplotPalettesprepareParameters2prepareParameters4processClippingtransparent
Dependencies:abindAnnotationDbiAnnotationFilteraskpassbackportsbamsignalsbase64encbezierBHBiobaseBiocBaseUtilsBiocGenericsBiocIOBiocParallelBiostringsbiovizBasebitbit64bitopsblobBSgenomebslibcachemcheckmatecigarillocliclustercodetoolscolorspacecpp11crayoncurldata.tableDBIDelayedArraydichromatdigestensembldbevaluatefarverfastmapfontawesomeforeignformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2gluegridExtragtablehighrHmischtmlTablehtmltoolshtmlwidgetshttrIRangesisobandjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlatticelazyevallifecyclemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimennetopensslpkgconfigpngProtGenericsR6rappdirsRColorBrewerRcppRCurlregioneRrestfulrRhtslibrjsonrlangrmarkdownrpartRsamtoolsRSQLiterstudioapirtracklayerS4ArraysS4VectorsS7sassscalesSeqinfosnowSparseArraystringistringrSummarizedExperimentsystinytexUCSC.utilsVariantAnnotationvctrsviridisLitewithrxfunXMLXVectoryaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| addGeneNames | addGeneNames |
| autotrack | autotrack |
| colByCategory | colByCategory |
| colByChr | colByChr |
| colByRegion | colByRegion |
| colByValue | colByValue |
| darker | darker |
| filterParams | filterParams |
| findIntersections | findIntersections |
| getChromosomeNamesBoundingBox | getChromosomeNamesBoundingBox |
| getColorSchemas | getColorSchemas |
| getCytobandColors | getCytobandColors |
| getCytobands | getCytobands |
| getDataPanelBoundingBox | getDataPanelBoundingBox |
| getDefaultParameters | getDefaultPlotParams |
| getMainTitleBoundingBox | getMainTitleBoundingBox |
| getTextSize | getTextSize |
| getVariantsColors | getVariantsColors |
| horizonColors | horizonColors |
| is.color | is.color |
| kpAbline | kpAbline |
| kpAddBaseNumbers | kpAddBaseNumbers |
| kpAddChromosomeNames | kpAddChromosomeNames |
| kpAddChromosomeSeparators | kpAddChromosomeSeparators |
| kpAddColorRect | kpAddColorRect |
| kpAddCytobandLabels | kpAddCytobandLabels |
| kpAddCytobands | kpAddCytobands |
| kpAddCytobandsAsLine | kpAddCytobandsAsLine |
| kpAddLabels | kpAddLabels |
| kpAddMainTitle | kpAddMainTitle |
| kpArea | kpArea |
| kpArrows | kpArrows |
| kpAxis | kpAxis |
| kpBars | kpBars |
| kpDataBackground | kpDataBackground |
| kpHeatmap | kpHeatmap |
| kpLines | kpLines |
| kpPlotBAMCoverage | kpPlotBAMCoverage |
| kpPlotBAMDensity | kpPlotBAMDensity |
| kpPlotBigWig | kpPlotBigWig |
| kpPlotCoverage | kpPlotCoverage |
| kpPlotDensity | kpPlotDensity |
| kpPlotGenes | kpPlotGenes |
| kpPlotHorizon | kpPlotHorizon |
| kpPlotLinks | kpPlotLinks |
| kpPlotLoess | kpPlotLoess |
| kpPlotManhattan | kpPlotManhattan |
| kpPlotMarkers | kpPlotMarkers |
| kpPlotNames | kpPlotNames |
| kpPlotRainfall | kpPlotRainfall |
| kpPlotRegions | kpPlotRegions |
| kpPlotRibbon | kpPlotRibbon |
| kpPlotTranscripts | kpPlotTranscripts |
| kpPoints | kpPoints |
| kpPolygon | kpPolygon |
| kpRect | kpRect |
| kpSegments | kpSegments |
| kpText | kpText |
| lighter | lighter |
| makeGenesDataFromTxDb | makeGenesDataFromTxDb |
| mergeTranscripts | mergeTranscripts |
| plotDefaultPlotParameters | plotDefaultPlotParams |
| plotKaryotype | plotKaryotype |
| plotPalette | plotPalettes |
| prepareParameters2 | prepareParameters2 |
| prepareParameters4 | prepareParameters4 |
| processClipping | processClipping |
| transparent | transparent |
