Package: biovizBase 1.53.0

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]

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biovizBase.pdf |biovizBase.html✨
biovizBase/json (API)
NEWS

# Install 'biovizBase' in R:

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

Datasets:

crc.gr - CRC
crc1.GeRL - Crc1.GeRL
darned_hg19_subset500 - Subset of RNA editing sites in hg19...
genesymbol - Gene symbols with position...
hg19Ideogram - Hg19 ideogram without cytoband information...
hg19IdeogramCyto - Hg19 ideogram with cytoband information...
hg19sub - CRC
ideo - Ideogram without cytoband information
ideoCyto - Ideogram with cytoband information
mut.gr - CRC

On BioConductor:biovizBase-1.53.0(bioc 3.20)biovizBase-1.52.0(bioc 3.19)

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

bioconductor-package

49 exports 5.60 score 125 dependencies 74 dependents 1 mentions

Last updated 2 months agofrom:a1b7afc09a

Exports:addStepping blind.pal.info brewer.pal.blind.info colorBlindSafePal containLetters crunch dichromat.pal.blind.info estimateCoverage flatGrl GCcontent genBlindPalInfo genBrewerBlindPalInfo genDichromatPalInfo getBioColor getFormalNames getGaps getIdeoGR getIdeogram getScale getXLab getXScale getYLab is_coord_genome is_coord_truncate_gaps isIdeogram isJunctionRead isMatchedWithModel isSimpleIdeogram maxGap mold parseArgsForAes parseArgsForNonAes pileupAsGRanges pileupGRangesAsVariantTable plotColorLegend showColor shrinkageFun splitByFacets strip_formula_dots subsetArgsByFormals transformDfToGr transformGRangesForEvenSpace transformToBarInCircle transformToCircle transformToDf transformToGenome transformToLinkInCircle transformToRectInCircle transformToSegInCircle

Dependencies:abind AnnotationDbi AnnotationFilter askpass backports base64enc BH Biobase BiocGenerics BiocIO BiocParallel Biostrings 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 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 RCurl 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

An Introduction to biovizBase

Rendered fromintro.Rnwusingutils::Sweaveon Jun 13 2024.

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
biovizBase is a package which provides utilities and color scheme...	biovizBase-package biovizBase
Adding disjoint levels to a GenomicRanges object	addStepping addStepping,GenomicRanges-method
Color blind safe palette generator	blind.pal.info brewer.pal.blind.info colorBlindSafePal dichromat.pal.blind.info genBlindPalInfo genBrewerBlindPalInfo genDichromatPalInfo
Checking if string contains letters or not	containLetters
CRC	CRC crc.gr hg19sub mut.gr
crc1.GeRL	crc1.GeRL
Fetching GRanges from various data source	crunch crunch,BamFile-method crunch,EnsDb-method crunch,GAlignments-method crunch,TxDb-method
Subset of RNA editing sites in hg19...	darned_hg19_subset500
Estimation of Coverage	estimateCoverage estimateCoverage,BamFile-method
Transform GRangesList to GRanges	flatGrl
GC content computation for BSgenome	GCcontent
Gene symbols with position...	genesymbol
Color scheme getter for biological data	getBioColor
Get formals from functions	getFormalNames
get gaps for a stepping transformed GRanges object	getGaps getGaps,GRanges-method
Get ideogram information	getIdeoGR
Get ideogram.	getIdeogram
Get scale information from a GRanges	getScale
get x scale breaks and labels	getXScale getXScale,GRanges-method
parse x and y label information from a specific object	getXLab 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 information	ideo
ideogram with cytoband information	ideoCyto
Ideogram checking	isIdeogram
Utils for Splicing Summary	isJunctionRead isMatchedWithModel
Simple ideogram checking	isSimpleIdeogram
Estimated max gaps	maxGap maxGap,GenomicRanges-method
mold data into data.frame	mold 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 arguments	parseArgsForAes parseArgsForNonAes
Summarize reads for certain region	pileupAsGRanges
Mismatch summary	pileupGRangesAsVariantTable
Show colors	plotColorLegend
Show colors	showColor
Shrinkage function	is_coord_truncate_gaps shrinkageFun shrinkageFun,GenomicRanges-method shrinkageFun,IRanges-method
split a GRanges by formula	splitByFacets splitByFacets,GRanges,formula-method splitByFacets,GRanges,GRanges-method splitByFacets,GRanges,missing-method splitByFacets,GRanges,NULL-method
strip dots around a formula variables	strip_formula_dots
Subset list of arguments by functions	subsetArgsByFormals
Transform GRanges with New Coordinates	transformGRangesForEvenSpace
Transform GRanges to different coordinates and layout	is_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