Package: biovizBase 1.61.0

Michael Lawrence

biovizBase: Basic graphic utilities for visualization of genomic data.

The biovizBase package is designed to provide a set of utilities, color schemes and conventions for genomic data. It serves as the base for various high-level packages for biological data visualization. This saves development effort and encourages consistency.

Authors:Tengfei Yin [aut], Michael Lawrence [aut, ths, cre], Dianne Cook [aut, ths], Johannes Rainer [ctb]

biovizBase_1.61.0.tar.gz
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manual.pdf |manual.html✨
card.svg |card.png
biovizBase/json (API)
NEWS

# Install 'biovizBase' in R:
install.packages('biovizBase', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))
Datasets:

On BioConductor:biovizBase-1.61.0(bioc 3.24)biovizBase-1.60.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

infrastructurevisualizationpreprocessing

8.57 score 76 packages 442 scripts 9.2k downloads 1 mentions 49 exports 118 dependencies

Last updated from:c17f233cf1. Checks:1 ERROR, 11 WARNING, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksERROR333
linux-devel-arm64WARNING475
linux-devel-x86_64WARNING602
source / vignettesOK466
linux-release-arm64WARNING501
linux-release-x86_64WARNING593
macos-release-arm64WARNING511
macos-release-x86_64WARNING690
macos-oldrel-arm64WARNING301
macos-oldrel-x86_64WARNING716
windows-develWARNING462
windows-releaseWARNING437
windows-oldrelWARNING423
wasm-releaseOK284

Exports:addSteppingblind.pal.infobrewer.pal.blind.infocolorBlindSafePalcontainLetterscrunchdichromat.pal.blind.infoestimateCoverageflatGrlGCcontentgenBlindPalInfogenBrewerBlindPalInfogenDichromatPalInfogetBioColorgetFormalNamesgetGapsgetIdeoGRgetIdeogramgetScalegetXLabgetXScalegetYLabis_coord_genomeis_coord_truncate_gapsisIdeogramisJunctionReadisMatchedWithModelisSimpleIdeogrammaxGapmoldparseArgsForAesparseArgsForNonAespileupAsGRangespileupGRangesAsVariantTableplotColorLegendshowColorshrinkageFunsplitByFacetsstrip_formula_dotssubsetArgsByFormalstransformDfToGrtransformGRangesForEvenSpacetransformToBarInCircletransformToCircletransformToDftransformToGenometransformToLinkInCircletransformToRectInCircletransformToSegInCircle

Dependencies:abindAnnotationDbiAnnotationFilteraskpassbackportsbase64encBHBiobaseBiocBaseUtilsBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobBSgenomebslibcachemcheckmatecigarillocliclustercodetoolscolorspacecpp11crayoncurldata.tableDBIDelayedArraydichromatdigestensembldbevaluatefarverfastmapfontawesomeforeignformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2gluegridExtragtablehighrHmischtmlTablehtmltoolshtmlwidgetshttrIRangesisobandjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlatticelazyevallifecyclemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimennetopensslpkgconfigpngProtGenericsR6rappdirsRColorBrewerRCurlrestfulrRhtslibrjsonrlangrmarkdownrpartRsamtoolsRSQLiterstudioapirtracklayerS4ArraysS4VectorsS7sassscalesSeqinfosnowSparseArraystringistringrSummarizedExperimentsystinytexUCSC.utilsVariantAnnotationvctrsviridisLitewithrxfunXMLXVectoryaml

An Introduction to biovizBase

Rendered fromintro.Rnwusingutils::Sweaveon May 29 2026.

Last update: 2014-04-17
Started: 2013-11-01

Readme and manuals

Help Manual

Help pageTopics
biovizBase is a package which provides utilities and color scheme...biovizBase-package biovizBase
Adding disjoint levels to a GenomicRanges objectaddStepping addStepping,GenomicRanges-method
Color blind safe palette generatorblind.pal.info brewer.pal.blind.info colorBlindSafePal dichromat.pal.blind.info genBlindPalInfo genBrewerBlindPalInfo genDichromatPalInfo
Checking if string contains letters or notcontainLetters
CRCCRC crc.gr hg19sub mut.gr
crc1.GeRLcrc1.GeRL
Fetching GRanges from various data sourcecrunch crunch,BamFile-method crunch,EnsDb-method crunch,GAlignments-method crunch,TxDb-method
Subset of RNA editing sites in hg19...darned_hg19_subset500
Estimation of CoverageestimateCoverage estimateCoverage,BamFile-method
Transform GRangesList to GRangesflatGrl
GC content computation for BSgenomeGCcontent
Gene symbols with position...genesymbol
Color scheme getter for biological datagetBioColor
Get formals from functionsgetFormalNames
get gaps for a stepping transformed GRanges objectgetGaps getGaps,GRanges-method
Get ideogram informationgetIdeoGR
Get ideogram.getIdeogram
Get scale information from a GRangesgetScale
get x scale breaks and labelsgetXScale getXScale,GRanges-method
parse x and y label information from a specific objectgetXLab getXLab,GAlignments-method getXLab,GRanges-method getXLab,GRangesList-method getXLab-method getYLab getYLab,TxDb-method
Hg19 ideogram without cytoband information...hg19Ideogram
Hg19 ideogram with cytoband information...hg19IdeogramCyto
ideogram without cytoband informationideo
ideogram with cytoband informationideoCyto
Ideogram checkingisIdeogram
Utils for Splicing SummaryisJunctionRead isMatchedWithModel
Simple ideogram checkingisSimpleIdeogram
Estimated max gapsmaxGap maxGap,GenomicRanges-method
mold data into data.framemold mold,eSet-method mold,ExpressionSet-method mold,GRanges-method mold,GRangesList-method mold,IRanges-method mold,matrix-method mold,RangedSummarizedExperiment-method mold,Rle-method mold,RleList-method mold,Seqinfo-method mold,SummarizedExperiment-method mold,Views-method mold,VRanges-method
Utils for parsing (un)evaluated argumentsparseArgsForAes parseArgsForNonAes
Summarize reads for certain regionpileupAsGRanges
Mismatch summarypileupGRangesAsVariantTable
Show colorsplotColorLegend
Show colorsshowColor
Shrinkage functionis_coord_truncate_gaps shrinkageFun shrinkageFun,GenomicRanges-method shrinkageFun,IRanges-method
split a GRanges by formulasplitByFacets splitByFacets,GRanges,formula-method splitByFacets,GRanges,GRanges-method splitByFacets,GRanges,missing-method splitByFacets,GRanges,NULL-method
strip dots around a formula variablesstrip_formula_dots
Subset list of arguments by functionssubsetArgsByFormals
Transform GRanges with New CoordinatestransformGRangesForEvenSpace
Transform GRanges to different coordinates and layoutis_coord_genome transformDfToGr transformToArch transformToArch,GRanges-method transformToBarInCircle transformToCircle transformToDf transformToDf,GRanges-method transformToDf-method transformToGenome transformToGenome,GRanges-method transformToGenome,GRangesList-method transformToLinkInCircle transformToRectInCircle transformToSegInCircle