# Basic graphic utilities for visualization of genomic data.

## Documentation for package ‘biovizBase’ version 1.16.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

biovizBase-package | biovizBase is a package which provides utilities and color scheme...
addStepping | Adding disjoint levels to a GenomicRanges object
addStepping-method | Adding disjoint levels to a GenomicRanges object
biovizBase | biovizBase is a package which provides utilities and color scheme...
blind.pal.info | Color blind safe palette generator
brewer.pal.blind.info | Color blind safe palette generator
colorBlindSafePal | Color blind safe palette generator
containLetters | Checking if string contains letters or not
CRC | CRC
crc.gr | CRC
crc1.GeRL | crc1.GeRL
crunch | Fetching GRanges from various data source
crunch-method | Fetching GRanges from various data source
darned_hg19_subset500 | Subset of RNA editing sites in hg19...
dichromat.pal.blind.info | Color blind safe palette generator
estimateCoverage | Estimation of Coverage
estimateCoverage-method | Estimation of Coverage
flatGrl | Transform GRangesList to GRanges
GCcontent | GC content computation for BSgenome
genBlindPalInfo | Color blind safe palette generator
genBrewerBlindPalInfo | Color blind safe palette generator
genDichromatPalInfo | Color blind safe palette generator
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
getGaps-method | get gaps for a stepping transformed GRanges object
getIdeoGR | Get ideogram information
getIdeogram | Get ideogram.
getScale | Get scale information from a GRanges
getXLab | parse x and y label information from a specific object
getXLab-method | parse x and y label information from a specific object
getXScale | get x scale breaks and labels
getXScale-method | get x scale breaks and labels
getYLab | parse x and y label information from a specific object
getYLab-method | parse x and y label information from a specific object
hg19Ideogram | Hg19 ideogram without cytoband information...
hg19IdeogramCyto | Hg19 ideogram with cytoband information...
hg19sub | CRC
ideo | ideogram without cytoband information
ideoCyto | ideogram with cytoband information
isIdeogram | Ideogram checking
isJunctionRead | Utils for Splicing Summary
isMatchedWithModel | Utils for Splicing Summary
isSimpleIdeogram | Simple ideogram checking
is_coord_genome | Transform GRanges to different coordinates and layout
is_coord_truncate_gaps | Shrinkage function
maxGap | Estimated max gaps
maxGap-method | Estimated max gaps
mold | mold data into data.frame
mold-method | mold data into data.frame
mut.gr | CRC
parseArgsForAes | Utils for parsing (un)evaluated arguments
parseArgsForNonAes | Utils for parsing (un)evaluated arguments
pileupAsGRanges | Summarize reads for certain region
pileupGRangesAsVariantTable | Mismatch summary
plotColorLegend | Show colors
showColor | Show colors
shrinkageFun | Shrinkage function
shrinkageFun-method | Shrinkage function
splitByFacets | split a GRanges by formula
splitByFacets-method | split a GRanges by formula
strip_formula_dots | strip dots around a formula variables
subsetArgsByFormals | Subset list of arguments by functions
transformDfToGr | Transform GRanges to different coordinates and layout
transformGRangesForEvenSpace | Transform GRanges with New Coordinates
transformToArch | Transform GRanges to different coordinates and layout
transformToArch-method | Transform GRanges to different coordinates and layout
transformToBarInCircle | Transform GRanges to different coordinates and layout
transformToCircle | Transform GRanges to different coordinates and layout
transformToDf | Transform GRanges to different coordinates and layout
transformToDf-method | Transform GRanges to different coordinates and layout
transformToGenome | Transform GRanges to different coordinates and layout
transformToGenome-method | Transform GRanges to different coordinates and layout
transformToLinkInCircle | Transform GRanges to different coordinates and layout
transformToRectInCircle | Transform GRanges to different coordinates and layout
transformToSegInCircle | Transform GRanges to different coordinates and layout