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.

AuthorTengfei Yin [aut], Michael Lawrence [aut, ths, cre], Dianne Cook [aut, ths], Johannes Rainer [ctb]
Date of publicationNone
MaintainerMichael Lawrence <lawrence.michael@gene.com>
LicenseArtistic-2.0
Version1.22.0

View on Bioconductor

Man pages

addStepping-method: Adding disjoint levels to a GenomicRanges object

aes-utils: Utils for parsing (un)evaluated arguments

biovizBase-package: biovizBase is a package which provides utilities and color...

colorBlindSafePal: Color blind safe palette generator

containLetters: Checking if string contains letters or not

CRC: CRC

crc1.GeRL: crc1.GeRL

crunch-method: Fetching GRanges from various data source

darned_hg19_subset500: Subset of RNA editing sites in hg19...

estimateCoverage-method: Estimation of Coverage

flatGrl: Transform GRangesList to GRanges

GCcontent: GC content computation for BSgenome

genesymbol: Gene symbols with position...

getBioColor: Color scheme getter for biological data

getFormalNames: Get formals from functions

getGaps: get gaps for a stepping transformed GRanges object

getIdeoGR: Get ideogram information

getIdeogram: Get ideogram.

getScale: Get scale information from a GRanges

hg19Ideogram: Hg19 ideogram without cytoband information...

hg19IdeogramCyto: Hg19 ideogram with cytoband information...

ideo: ideogram without cytoband information

ideoCyto: ideogram with cytoband information

isIdeogram: Ideogram checking

isMatchedWithModel: Utils for Splicing Summary

isSimpleIdeogram: Simple ideogram checking

labs: parse x and y label information from a specific object

maxGap-method: Estimated max gaps

mold-method: mold data into data.frame

pileupAsGRanges: Summarize reads for certain region

pileupGRangesAsVariantTable: Mismatch summary

plotColorLegend: Show colors

scale: get x scale breaks and labels

showColor: Show colors

shrinkageFun-method: Shrinkage function

splitByFacets-method: split a GRanges by formula

strip_formula_dots: strip dots around a formula variables

subsetArgsByFormals: Subset list of arguments by functions

transform: Transform GRanges to different coordinates and layout

transformGRangesForEvenSpace: Transform GRanges with New Coordinates

Functions

addStepping Man page
addStepping,GenomicRanges-method Man page
biovizBase Man page
biovizBase-package Man page
biovizBase-package Man page
blind.pal.info Man page
brewer.pal.blind.info Man page
colorBlindSafePal Man page
containLetters Man page
CRC Man page
crc1.GeRL Man page
crc1.GeRL Man page
crc.gr Man page
crunch Man page
crunch,BamFile-method Man page
crunch,EnsDb-method Man page
crunch,GAlignments-method Man page
crunch,TxDb-method Man page
darned_hg19_subset500 Man page
darned_hg19_subset500 Man page
dichromat.pal.blind.info Man page
estimateCoverage Man page
estimateCoverage,BamFile-method Man page
flatGrl Man page
GCcontent Man page
genBlindPalInfo Man page
genBrewerBlindPalInfo Man page
genDichromatPalInfo Man page
genesymbol Man page
genesymbol Man page
getBioColor Man page
getFormalNames Man page
getGaps Man page
getGaps,GRanges-method Man page
getIdeoGR Man page
getIdeogram Man page
getScale Man page
getXLab Man page
getXLab,GAlignments-method Man page
getXLab,GRangesList-method Man page
getXLab,GRanges-method Man page
getXLab-method Man page
getXScale Man page
getXScale,GRanges-method Man page
getYLab Man page
getYLab,TxDb-method Man page
hg19Ideogram Man page
hg19Ideogram Man page
hg19IdeogramCyto Man page
hg19IdeogramCyto Man page
hg19sub Man page
ideo Man page
ideoCyto Man page
is_coord_genome Man page
is_coord_truncate_gaps Man page
isIdeogram Man page
isJunctionRead Man page
isMatchedWithModel Man page
isSimpleIdeogram Man page
maxGap Man page
maxGap,GenomicRanges-method Man page
mold Man page
mold,eSet-method Man page
mold,ExpressionSet-method Man page
mold,GRangesList-method Man page
mold,GRanges-method Man page
mold,IRanges-method Man page
mold,matrix-method Man page
mold,RangedSummarizedExperiment-method Man page
mold,RleList-method Man page
mold,Rle-method Man page
mold,Seqinfo-method Man page
mold,SummarizedExperiment-method Man page
mold,Views-method Man page
mold,VRanges-method Man page
mut.gr Man page
parseArgsForAes Man page
parseArgsForNonAes Man page
pileupAsGRanges Man page
pileupGRangesAsVariantTable Man page
plotColorLegend Man page
showColor Man page
shrinkageFun Man page
shrinkageFun,GenomicRanges-method Man page
shrinkageFun,IRanges-method Man page
splitByFacets Man page
splitByFacets,GRanges,formula-method Man page
splitByFacets,GRanges,GRanges-method Man page
splitByFacets,GRanges,missing-method Man page
splitByFacets,GRanges,NULL-method Man page
strip_formula_dots Man page
subsetArgsByFormals Man page
transformDfToGr Man page
transformGRangesForEvenSpace Man page
transformToArch Man page
transformToArch,GRanges-method Man page
transformToBarInCircle Man page
transformToCircle Man page
transformToDf Man page
transformToDf,GRanges-method Man page
transformToDf-method Man page
transformToGenome Man page
transformToGenome,GRangesList-method Man page
transformToGenome,GRanges-method Man page
transformToLinkInCircle Man page
transformToRectInCircle Man page
transformToSegInCircle Man page

Files

biovizBase/DESCRIPTION
biovizBase/NAMESPACE
biovizBase/NEWS
biovizBase/R
biovizBase/R/AllGenerics.R biovizBase/R/addStepping-method.R biovizBase/R/aes.R biovizBase/R/biovizBase-package.R biovizBase/R/color.R biovizBase/R/coverage.R biovizBase/R/crunch-method.R biovizBase/R/facets-method.R biovizBase/R/getFragLength-method.R biovizBase/R/ideogram.R biovizBase/R/labs.R biovizBase/R/maxGap-method.R biovizBase/R/mold-method.R biovizBase/R/original.R biovizBase/R/pileup.R biovizBase/R/scale.R biovizBase/R/shrinkageFun-method.R biovizBase/R/spliceSummary-method.R biovizBase/R/transform.R biovizBase/R/utils.R biovizBase/R/zzz.R
biovizBase/build
biovizBase/build/vignette.rds
biovizBase/data
biovizBase/data/CRC.rda
biovizBase/data/crc1.GeRL.rda
biovizBase/data/darned_hg19_subset500.rda
biovizBase/data/genesymbol.rda
biovizBase/data/hg19Ideogram.rda
biovizBase/data/hg19IdeogramCyto.rda
biovizBase/data/ideo.rda
biovizBase/data/ideoCyto.rda
biovizBase/inst
biovizBase/inst/doc
biovizBase/inst/doc/intro.R
biovizBase/inst/doc/intro.Rnw
biovizBase/inst/doc/intro.pdf
biovizBase/inst/examples
biovizBase/inst/examples/color.R
biovizBase/inst/examples/data-gen.R
biovizBase/inst/examples/test.R
biovizBase/inst/extdata
biovizBase/inst/extdata/17-1409-CEU-brca1.vcf.bgz
biovizBase/inst/extdata/17-1409-CEU-brca1.vcf.bgz.tbi
biovizBase/inst/extdata/SRR027894subRBM17.bam
biovizBase/inst/extdata/SRR027894subRBM17.bam.bai
biovizBase/inst/extdata/crc-rearrangment.csv
biovizBase/inst/extdata/crc1-missense.csv
biovizBase/inst/extdata/plink.assoc.sub.txt
biovizBase/inst/extdata/wg-brca1.sorted.bam
biovizBase/inst/extdata/wg-brca1.sorted.bam.bai
biovizBase/inst/unitTests
biovizBase/inst/unitTests/test_ensdb.R
biovizBase/man
biovizBase/man/CRC.Rd biovizBase/man/GCcontent.Rd biovizBase/man/addStepping-method.Rd biovizBase/man/aes-utils.Rd biovizBase/man/biovizBase-package.Rd biovizBase/man/colorBlindSafePal.Rd biovizBase/man/containLetters.Rd biovizBase/man/crc1.GeRL.Rd biovizBase/man/crunch-method.Rd biovizBase/man/darned_hg19_subset500.Rd biovizBase/man/estimateCoverage-method.Rd biovizBase/man/flatGrl.Rd biovizBase/man/genesymbol.Rd biovizBase/man/getBioColor.Rd biovizBase/man/getFormalNames.Rd biovizBase/man/getGaps.Rd biovizBase/man/getIdeoGR.Rd biovizBase/man/getIdeogram.Rd biovizBase/man/getScale.Rd biovizBase/man/hg19Ideogram.Rd biovizBase/man/hg19IdeogramCyto.Rd biovizBase/man/ideo.Rd biovizBase/man/ideoCyto.Rd biovizBase/man/isIdeogram.Rd biovizBase/man/isMatchedWithModel.Rd biovizBase/man/isSimpleIdeogram.Rd biovizBase/man/labs.Rd biovizBase/man/maxGap-method.Rd biovizBase/man/mold-method.Rd biovizBase/man/pileupAsGRanges.Rd biovizBase/man/pileupGRangesAsVariantTable.Rd biovizBase/man/plotColorLegend.Rd biovizBase/man/scale.Rd biovizBase/man/showColor.Rd biovizBase/man/shrinkageFun-method.Rd biovizBase/man/splitByFacets-method.Rd biovizBase/man/strip_formula_dots.Rd biovizBase/man/subsetArgsByFormals.Rd biovizBase/man/transform.Rd biovizBase/man/transformGRangesForEvenSpace.Rd
biovizBase/src
biovizBase/src/R_init_biovizBase.c
biovizBase/src/bin_offsets.c
biovizBase/src/bin_offsets.h
biovizBase/tests
biovizBase/tests/runTests.R
biovizBase/vignettes
biovizBase/vignettes/intro-shrink-single.pdf
biovizBase/vignettes/intro-shrinkageFun.pdf
biovizBase/vignettes/intro.Rnw

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

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