Package: karyoploteR 1.31.0

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_1.31.0.tar.gz
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Peer review:

Bug tracker:https://github.com/bernatgel/karyoploter/issues

On BioConductor:karyoploteR-1.31.0(bioc 3.20)karyoploteR-1.30.0(bioc 3.19)

bioconductor-package

68 exports 1.80 score 130 dependencies 4 dependents 50 mentions

Last updated 2 months agofrom:574fd7a5d3

Exports:addGeneNamesautotrackcolByCategorycolByChrcolByRegioncolByValuedarkerfilterParamsfindIntersectionsgetChromosomeNamesBoundingBoxgetColorSchemasgetCytobandColorsgetCytobandsgetDataPanelBoundingBoxgetDefaultPlotParamsgetMainTitleBoundingBoxgetTextSizegetVariantsColorshorizonColorsis.colorkpAblinekpAddBaseNumberskpAddChromosomeNameskpAddChromosomeSeparatorskpAddColorRectkpAddCytobandLabelskpAddCytobandskpAddCytobandsAsLinekpAddLabelskpAddMainTitlekpAreakpArrowskpAxiskpBarskpDataBackgroundkpHeatmapkpLineskpPlotBAMCoveragekpPlotBAMDensitykpPlotBigWigkpPlotCoveragekpPlotDensitykpPlotGeneskpPlotHorizonkpPlotLinkskpPlotLoesskpPlotManhattankpPlotMarkerskpPlotNameskpPlotRainfallkpPlotRegionskpPlotRibbonkpPlotTranscriptskpPointskpPolygonkpRectkpSegmentskpTextlightermakeGenesDataFromTxDbmergeTranscriptsplotDefaultPlotParamsplotKaryotypeplotPalettesprepareParameters2prepareParameters4processClippingtransparent

Dependencies:abindAnnotationDbiAnnotationFilteraskpassbackportsbamsignalsbase64encbezierBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbiovizBasebitbit64bitopsblobBSgenomebslibcachemcheckmatecliclustercodetoolscolorspacecpp11crayoncurldata.tableDBIDelayedArraydichromatdigestensembldbevaluatefansifarverfastmapfontawesomeforeignformatRFormulafsfutile.loggerfutile.optionsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2gluegridExtragtablehighrHmischtmlTablehtmltoolshtmlwidgetshttrIRangesisobandjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlatticelazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmennetopensslpillarpkgconfigplogrpngProtGenericsR6rappdirsRColorBrewerRcppRCurlregioneRrestfulrRhtslibrjsonrlangrmarkdownrpartRsamtoolsRSQLiterstudioapirtracklayerS4ArraysS4VectorssassscalessnowSparseArraystringistringrSummarizedExperimentsystibbletinytexUCSC.utilsutf8VariantAnnotationvctrsviridisviridisLitewithrxfunXMLXVectoryamlzlibbioc