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:
karyoploteR_1.33.0.tar.gz
karyoploteR_1.33.0.zip(r-4.5)karyoploteR_1.33.0.zip(r-4.4)karyoploteR_1.33.0.zip(r-4.3)
karyoploteR_1.33.0.tgz(r-4.4-any)karyoploteR_1.33.0.tgz(r-4.3-any)
karyoploteR_1.33.0.tar.gz(r-4.5-noble)karyoploteR_1.33.0.tar.gz(r-4.4-noble)
karyoploteR_1.33.0.tgz(r-4.4-emscripten)karyoploteR_1.33.0.tgz(r-4.3-emscripten)
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
Last updated 2 months agofrom:4e6d89c3e7. Checks:OK: 1 ERROR: 2 NOTE: 4. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 29 2024 |
| R-4.5-win | ERROR | Nov 29 2024 |
| R-4.5-linux | ERROR | Nov 29 2024 |
| R-4.4-win | NOTE | Nov 29 2024 |
| R-4.4-mac | NOTE | Nov 29 2024 |
| R-4.3-win | NOTE | Nov 29 2024 |
| R-4.3-mac | NOTE | Nov 29 2024 |
Exports:addGeneNamesautotrackcolByCategorycolByChrcolByRegioncolByValuedarkerfilterParamsfindIntersectionsgetChromosomeNamesBoundingBoxgetColorSchemasgetCytobandColorsgetCytobandsgetDataPanelBoundingBoxgetDefaultPlotParamsgetMainTitleBoundingBoxgetTextSizegetVariantsColorshorizonColorsis.colorkpAblinekpAddBaseNumberskpAddChromosomeNameskpAddChromosomeSeparatorskpAddColorRectkpAddCytobandLabelskpAddCytobandskpAddCytobandsAsLinekpAddLabelskpAddMainTitlekpAreakpArrowskpAxiskpBarskpDataBackgroundkpHeatmapkpLineskpPlotBAMCoveragekpPlotBAMDensitykpPlotBigWigkpPlotCoveragekpPlotDensitykpPlotGeneskpPlotHorizonkpPlotLinkskpPlotLoesskpPlotManhattankpPlotMarkerskpPlotNameskpPlotRainfallkpPlotRegionskpPlotRibbonkpPlotTranscriptskpPointskpPolygonkpRectkpSegmentskpTextlightermakeGenesDataFromTxDbmergeTranscriptsplotDefaultPlotParamsplotKaryotypeplotPalettesprepareParameters2prepareParameters4processClippingtransparent
Dependencies:abindAnnotationDbiAnnotationFilteraskpassbackportsbamsignalsbase64encbezierBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbiovizBasebitbit64bitopsblobBSgenomebslibcachemcheckmatecliclustercodetoolscolorspacecpp11crayoncurldata.tableDBIDelayedArraydichromatdigestensembldbevaluatefansifarverfastmapfontawesomeforeignformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2gluegridExtragtablehighrHmischtmlTablehtmltoolshtmlwidgetshttrIRangesisobandjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlatticelazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmennetopensslpillarpkgconfigplogrpngProtGenericsR6rappdirsRColorBrewerRcppRCurlregioneRrestfulrRhtslibrjsonrlangrmarkdownrpartRsamtoolsRSQLiterstudioapirtracklayerS4ArraysS4VectorssassscalessnowSparseArraystringistringrSummarizedExperimentsystibbletinytexUCSC.utilsutf8VariantAnnotationvctrsviridisviridisLitewithrxfunXMLXVectoryamlzlibbioc
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 |
