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)

visualization copynumbervariation sequencing coverage dnaseq chipseq methylseq dataimport onechannel bioconductor bioinformatics data-visualization genome genomics-visualization plotting-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.

Target	Result	Latest binary
Doc / Vignettes	OK	Jan 28 2025
R-4.5-win	ERROR	Jan 28 2025
R-4.5-mac	ERROR	Jan 28 2025
R-4.5-linux	ERROR	Jan 28 2025
R-4.4-win	NOTE	Jan 28 2025
R-4.4-mac	NOTE	Jan 28 2025
R-4.3-win	NOTE	Jan 28 2025
R-4.3-mac	NOTE	Jan 28 2025

Exports:addGeneNames autotrack colByCategory colByChr colByRegion colByValue darker filterParams findIntersections getChromosomeNamesBoundingBox getColorSchemas getCytobandColors getCytobands getDataPanelBoundingBox getDefaultPlotParams getMainTitleBoundingBox getTextSize getVariantsColors horizonColors is.color kpAbline kpAddBaseNumbers kpAddChromosomeNames kpAddChromosomeSeparators kpAddColorRect kpAddCytobandLabels kpAddCytobands kpAddCytobandsAsLine kpAddLabels kpAddMainTitle kpArea kpArrows kpAxis kpBars kpDataBackground kpHeatmap kpLines kpPlotBAMCoverage kpPlotBAMDensity kpPlotBigWig kpPlotCoverage kpPlotDensity kpPlotGenes kpPlotHorizon kpPlotLinks kpPlotLoess kpPlotManhattan kpPlotMarkers kpPlotNames kpPlotRainfall kpPlotRegions kpPlotRibbon kpPlotTranscripts kpPoints kpPolygon kpRect kpSegments kpText lighter makeGenesDataFromTxDb mergeTranscripts plotDefaultPlotParams plotKaryotype plotPalettes prepareParameters2 prepareParameters4 processClipping transparent

Dependencies:abind AnnotationDbi AnnotationFilter askpass backports bamsignals base64enc bezier BH Biobase BiocGenerics BiocIO BiocParallel Biostrings biovizBase bit bit64 bitops blob BSgenome bslib cachem checkmate cli cluster codetools colorspace cpp11 crayon curl data.table DBI DelayedArray dichromat digest ensembldb evaluate fansi farver fastmap fontawesome foreign formatR Formula fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges ggplot2 glue gridExtra gtable highr Hmisc htmlTable htmltools htmlwidgets httr IRanges isoband jquerylib jsonlite KEGGREST knitr labeling lambda.r lattice lazyeval lifecycle magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime munsell nlme nnet openssl pillar pkgconfig plogr png ProtGenerics R6 rappdirs RColorBrewer Rcpp RCurl regioneR restfulr Rhtslib rjson rlang rmarkdown rpart Rsamtools RSQLite rstudioapi rtracklayer S4Arrays S4Vectors sass scales snow SparseArray stringi stringr SummarizedExperiment sys tibble tinytex UCSC.utils utf8 VariantAnnotation vctrs viridis viridisLite withr xfun XML XVector yaml zlibbioc

karyoploteR: plot customizable linear genomes displaying arbitrary data

Bernat Gel ([email protected])

Rendered fromkaryoploteR.Rmdusingknitr::rmarkdownon Jan 28 2025.

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

Citation

Development and contributors

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