Package: karyoploteR 1.33.0

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:Bernat Gel [aut, cre]

karyoploteR_1.33.0.tar.gz
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karyoploteR.pdf |karyoploteR.html
karyoploteR/json (API)
NEWS

# 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-1.33.0(bioc 3.21)karyoploteR-1.32.0(bioc 3.20)

visualizationcopynumbervariationsequencingcoveragednaseqchipseqmethylseqdataimportonechannelbioconductorbioinformaticsdata-visualizationgenomegenomics-visualizationplotting-in-r

11.22 score 305 stars 4 packages 656 scripts 1.4k downloads 50 mentions 68 exports 131 dependencies

Last updated 4 months agofrom:4e6d89c3e7. Checks:1 OK, 3 ERROR, 4 NOTE. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKJan 28 2025
R-4.5-winERRORJan 28 2025
R-4.5-macERRORJan 28 2025
R-4.5-linuxERRORJan 28 2025
R-4.4-winNOTEJan 28 2025
R-4.4-macNOTEJan 28 2025
R-4.3-winNOTEJan 28 2025
R-4.3-macNOTEJan 28 2025

Exports:addGeneNamesautotrackcolByCategorycolByChrcolByRegioncolByValuedarkerfilterParamsfindIntersectionsgetChromosomeNamesBoundingBoxgetColorSchemasgetCytobandColorsgetCytobandsgetDataPanelBoundingBoxgetDefaultPlotParamsgetMainTitleBoundingBoxgetTextSizegetVariantsColorshorizonColorsis.colorkpAblinekpAddBaseNumberskpAddChromosomeNameskpAddChromosomeSeparatorskpAddColorRectkpAddCytobandLabelskpAddCytobandskpAddCytobandsAsLinekpAddLabelskpAddMainTitlekpAreakpArrowskpAxiskpBarskpDataBackgroundkpHeatmapkpLineskpPlotBAMCoveragekpPlotBAMDensitykpPlotBigWigkpPlotCoveragekpPlotDensitykpPlotGeneskpPlotHorizonkpPlotLinkskpPlotLoesskpPlotManhattankpPlotMarkerskpPlotNameskpPlotRainfallkpPlotRegionskpPlotRibbonkpPlotTranscriptskpPointskpPolygonkpRectkpSegmentskpTextlightermakeGenesDataFromTxDbmergeTranscriptsplotDefaultPlotParamsplotKaryotypeplotPalettesprepareParameters2prepareParameters4processClippingtransparent

Dependencies:abindAnnotationDbiAnnotationFilteraskpassbackportsbamsignalsbase64encbezierBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbiovizBasebitbit64bitopsblobBSgenomebslibcachemcheckmatecliclustercodetoolscolorspacecpp11crayoncurldata.tableDBIDelayedArraydichromatdigestensembldbevaluatefansifarverfastmapfontawesomeforeignformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2gluegridExtragtablehighrHmischtmlTablehtmltoolshtmlwidgetshttrIRangesisobandjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlatticelazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmennetopensslpillarpkgconfigplogrpngProtGenericsR6rappdirsRColorBrewerRcppRCurlregioneRrestfulrRhtslibrjsonrlangrmarkdownrpartRsamtoolsRSQLiterstudioapirtracklayerS4ArraysS4VectorssassscalessnowSparseArraystringistringrSummarizedExperimentsystibbletinytexUCSC.utilsutf8VariantAnnotationvctrsviridisviridisLitewithrxfunXMLXVectoryamlzlibbioc

karyoploteR: plot customizable linear genomes displaying arbitrary data

Rendered fromkaryoploteR.Rmdusingknitr::rmarkdownon Jan 28 2025.

Last update: 2021-08-30
Started: 2017-03-31

Readme and manuals

Help Manual

Help pageTopics
addGeneNamesaddGeneNames
autotrackautotrack
colByCategorycolByCategory
colByChrcolByChr
colByRegioncolByRegion
colByValuecolByValue
darkerdarker
filterParamsfilterParams
findIntersectionsfindIntersections
getChromosomeNamesBoundingBoxgetChromosomeNamesBoundingBox
getColorSchemasgetColorSchemas
getCytobandColorsgetCytobandColors
getCytobandsgetCytobands
getDataPanelBoundingBoxgetDataPanelBoundingBox
getDefaultParametersgetDefaultPlotParams
getMainTitleBoundingBoxgetMainTitleBoundingBox
getTextSizegetTextSize
getVariantsColorsgetVariantsColors
horizonColorshorizonColors
is.coloris.color
kpAblinekpAbline
kpAddBaseNumberskpAddBaseNumbers
kpAddChromosomeNameskpAddChromosomeNames
kpAddChromosomeSeparatorskpAddChromosomeSeparators
kpAddColorRectkpAddColorRect
kpAddCytobandLabelskpAddCytobandLabels
kpAddCytobandskpAddCytobands
kpAddCytobandsAsLinekpAddCytobandsAsLine
kpAddLabelskpAddLabels
kpAddMainTitlekpAddMainTitle
kpAreakpArea
kpArrowskpArrows
kpAxiskpAxis
kpBarskpBars
kpDataBackgroundkpDataBackground
kpHeatmapkpHeatmap
kpLineskpLines
kpPlotBAMCoveragekpPlotBAMCoverage
kpPlotBAMDensitykpPlotBAMDensity
kpPlotBigWigkpPlotBigWig
kpPlotCoveragekpPlotCoverage
kpPlotDensitykpPlotDensity
kpPlotGeneskpPlotGenes
kpPlotHorizonkpPlotHorizon
kpPlotLinkskpPlotLinks
kpPlotLoesskpPlotLoess
kpPlotManhattankpPlotManhattan
kpPlotMarkerskpPlotMarkers
kpPlotNameskpPlotNames
kpPlotRainfallkpPlotRainfall
kpPlotRegionskpPlotRegions
kpPlotRibbonkpPlotRibbon
kpPlotTranscriptskpPlotTranscripts
kpPointskpPoints
kpPolygonkpPolygon
kpRectkpRect
kpSegmentskpSegments
kpTextkpText
lighterlighter
makeGenesDataFromTxDbmakeGenesDataFromTxDb
mergeTranscriptsmergeTranscripts
plotDefaultPlotParametersplotDefaultPlotParams
plotKaryotypeplotKaryotype
plotPaletteplotPalettes
prepareParameters2prepareParameters2
prepareParameters4prepareParameters4
processClippingprocessClipping
transparenttransparent