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biovizBase (version 1.18.0)

Basic graphic utilities for visualization of genomic data.

Description

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.

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Version

Version

1.18.0

License

Artistic-2.0

Maintainer

Tengfei Yin

Last Published

February 15th, 2017

Functions in biovizBase (1.18.0)

biovizBase-package

biovizBase is a package which provides utilities and color scheme...
genesymbol

Gene symbols with position...
getBioColor

Color scheme getter for biological data
colorBlindSafePal

Color blind safe palette generator
mold

mold data into data.frame
pileupAsGRanges

Summarize reads for certain region
getXScale

get x scale breaks and labels
containLetters

Checking if string contains letters or not
CRC

CRC
flatGrl

Transform GRangesList to GRanges
GCcontent

GC content computation for BSgenome
ideoCyto

ideogram with cytoband information
strip_formula_dots

strip dots around a formula variables
isIdeogram

Ideogram checking
subsetArgsByFormals

Subset list of arguments by functions
estimateCoverage

Estimation of Coverage
darned_hg19_subset500

Subset of RNA editing sites in hg19...
isMatchedWithModel

Utils for Splicing Summary
getGaps

get gaps for a stepping transformed GRanges object
getFormalNames

Get formals from functions
isSimpleIdeogram

Simple ideogram checking
pileupGRangesAsVariantTable

Mismatch summary
showColor

Show colors
plotColorLegend

Show colors
getIdeoGR

Get ideogram information
getIdeogram

Get ideogram.
crc1.GeRL

crc1.GeRL
crunch

Fetching GRanges from various data source
hg19IdeogramCyto

Hg19 ideogram with cytoband information...
ideo

ideogram without cytoband information
transformToGenome

Transform GRanges to different coordinates and layout
transformGRangesForEvenSpace

Transform GRanges with New Coordinates
addStepping-method

Adding disjoint levels to a GenomicRanges object
getScale

Get scale information from a GRanges
parseArgsForAes

Utils for parsing (un)evaluated arguments
maxGap-method

Estimated max gaps
getYLab-method

parse x and y label information from a specific object
hg19Ideogram

Hg19 ideogram without cytoband information...
shrinkageFun-method

Shrinkage function
splitByFacets

split a GRanges by formula