biovizBase: Basic graphic utilities for visualization of genomic data.
Version 1.24.0

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.

Browse man pages Browse package API and functions Browse package files

AuthorTengfei Yin [aut], Michael Lawrence [aut, ths, cre], Dianne Cook [aut, ths], Johannes Rainer [ctb]
Bioconductor views Infrastructure Preprocessing Visualization
Date of publicationNone
MaintainerMichael Lawrence <lawrence.michael@gene.com>
LicenseArtistic-2.0
Version1.24.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("biovizBase")

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

AAAlphabetColor Source code
AminoAcidCodeColor Source code
CRC Man page
DNAAlphabetColor Source code
DNABasesColor Source code
DNABasesNColor Source code
GCcontent Man page Source code
IUPACCodeMapColor Source code
RNAAlphabetColor Source code
RNABasesColor Source code
RNABasesNColor Source code
addStepping Man page
addStepping,GenomicRanges-method Man page
biovizBase Man page
biovizBase-package Man page Man page
blind.pal.info Man page
brewer.pal.blind.info Man page
centroidPos Source code
check.integer Source code
checkFacetsRestrict Source code
colorBlindSafePal Man page Source code
colorschemes.num Source code
containLetters Man page Source code
crc.gr Man page
crc1.GeRL Man page 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
cytobandColor Source code
darned_hg19_subset500 Man page Man page
dichromat.pal.blind.info Man page
estimateCoverage Man page
estimateCoverage,BamFile-method Man page
fetch Source code
flatGrl Man page Source code
genBlindPalInfo Man page Source code
genBrewerBlindPalInfo Man page Source code
genDichromatPalInfo Man page Source code
genGenesymbolTable Source code
genSymbols Source code
genesymbol Man page Man page
getBioColor Man page Source code
getCytobandColor Source code
getFormalNames Man page Source code
getGaps Man page
getGaps,GRanges-method Man page
getIdeoGR Man page Source code
getIdeogram Man page Source code
getScale Man page Source code
getXLab Man page
getXLab,GAlignments-method Man page
getXLab,GRanges-method Man page
getXLab,GRangesList-method Man page
getXLab-method Man page
getXScale Man page
getXScale,GRanges-method Man page
getYLab Man page
getYLab,TxDb-method Man page
ggplot2_is.constant Source code
ggplot2_is_calculated_aes Source code
ggplot2_strip_dots Source code
hg19Ideogram Man page Man page
hg19IdeogramCyto Man page Man page
hg19sub Man page
ideo Man page
ideoCyto Man page
isFacetByOnlySeq Source code
isIdeogram Man page Source code
isJunctionRead Man page Source code
isMatchedWithModel Man page Source code
isSimpleIdeogram Man page Source code
is_coord_genome Man page Source code
is_coord_truncate_gaps Man page Source code
is_homo Source code
maxGap Man page
maxGap,GenomicRanges-method Man page
mold Man page
mold,ExpressionSet-method Man page
mold,GRanges-method Man page
mold,GRangesList-method Man page
mold,IRanges-method Man page
mold,RangedSummarizedExperiment-method Man page
mold,Rle-method Man page
mold,RleList-method Man page
mold,Seqinfo-method Man page
mold,SummarizedExperiment-method Man page
mold,VRanges-method Man page
mold,Views-method Man page
mold,eSet-method Man page
mold,matrix-method Man page
mut.gr Man page
newDataAfterFacetByGr Source code
onLoad Source code
parseArgsForAes Man page Source code
parseArgsForNonAes Man page Source code
pileupAsGRanges Man page Source code
pileupGRangesAsVariantTable Man page Source code
plotColorLegend Man page Source code
pspanGR Source code
rectifySeqlevelsStyle Source code
reduceNtruncate Source code
rescaleGr Source code
scanBamGRanges Source code
showColor Man page Source code
show_col2 Source code
shrinkageFun Man page
shrinkageFun,GenomicRanges-method Man page
shrinkageFun,IRanges-method Man page
splitByFacets Man page
splitByFacets,GRanges,GRanges-method Man page
splitByFacets,GRanges,NULL-method Man page
splitByFacets,GRanges,formula-method Man page
splitByFacets,GRanges,missing-method Man page
strandColor Source code
strip_formula_dots Man page Source code
subsetArgsByFormals Man page Source code
transformDfToGr Man page Source code
transformGRangesForEvenSpace Man page Source code
transformSeqinfo Source code
transformToArch Man page
transformToArch,GRanges-method Man page
transformToBarInCircle Man page Source code
transformToCircle Man page Source code
transformToDf Man page
transformToDf,GRanges-method Man page
transformToDf-method Man page
transformToEven Source code
transformToGenome Man page
transformToGenome,GRanges-method Man page
transformToGenome,GRangesList-method Man page
transformToLinkInCircle Man page Source code
transformToRectInCircle Man page Source code
transformToSegInCircle Man page Source code
transformToSegInCircle2 Source code

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/AllGenerics.R
R/addStepping-method.R
R/aes.R
R/biovizBase-package.R
R/color.R
R/coverage.R
R/crunch-method.R
R/facets-method.R
R/getFragLength-method.R
R/ideogram.R
R/labs.R
R/maxGap-method.R
R/mold-method.R
R/original.R
R/pileup.R
R/scale.R
R/shrinkageFun-method.R
R/spliceSummary-method.R
R/transform.R
R/utils.R
R/zzz.R
build
build/vignette.rds
data
data/CRC.rda
data/crc1.GeRL.rda
data/darned_hg19_subset500.rda
data/genesymbol.rda
data/hg19Ideogram.rda
data/hg19IdeogramCyto.rda
data/ideo.rda
data/ideoCyto.rda
inst
inst/doc
inst/doc/intro.R
inst/doc/intro.Rnw
inst/doc/intro.pdf
inst/examples
inst/examples/color.R
inst/examples/data-gen.R
inst/examples/test.R
inst/extdata
inst/extdata/17-1409-CEU-brca1.vcf.bgz
inst/extdata/17-1409-CEU-brca1.vcf.bgz.tbi
inst/extdata/SRR027894subRBM17.bam
inst/extdata/SRR027894subRBM17.bam.bai
inst/extdata/crc-rearrangment.csv
inst/extdata/crc1-missense.csv
inst/extdata/plink.assoc.sub.txt
inst/extdata/wg-brca1.sorted.bam
inst/extdata/wg-brca1.sorted.bam.bai
inst/unitTests
inst/unitTests/test_ensdb.R
man
man/CRC.Rd
man/GCcontent.Rd
man/addStepping-method.Rd
man/aes-utils.Rd
man/biovizBase-package.Rd
man/colorBlindSafePal.Rd
man/containLetters.Rd
man/crc1.GeRL.Rd
man/crunch-method.Rd
man/darned_hg19_subset500.Rd
man/estimateCoverage-method.Rd
man/flatGrl.Rd
man/genesymbol.Rd
man/getBioColor.Rd
man/getFormalNames.Rd
man/getGaps.Rd
man/getIdeoGR.Rd
man/getIdeogram.Rd
man/getScale.Rd
man/hg19Ideogram.Rd
man/hg19IdeogramCyto.Rd
man/ideo.Rd
man/ideoCyto.Rd
man/isIdeogram.Rd
man/isMatchedWithModel.Rd
man/isSimpleIdeogram.Rd
man/labs.Rd
man/maxGap-method.Rd
man/mold-method.Rd
man/pileupAsGRanges.Rd
man/pileupGRangesAsVariantTable.Rd
man/plotColorLegend.Rd
man/scale.Rd
man/showColor.Rd
man/shrinkageFun-method.Rd
man/splitByFacets-method.Rd
man/strip_formula_dots.Rd
man/subsetArgsByFormals.Rd
man/transform.Rd
man/transformGRangesForEvenSpace.Rd
src
src/R_init_biovizBase.c
src/bin_offsets.c
src/bin_offsets.h
tests
tests/runTests.R
vignettes
vignettes/intro-shrink-single.pdf
vignettes/intro-shrinkageFun.pdf
vignettes/intro.Rnw
biovizBase documentation built on May 20, 2017, 10:54 p.m.