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<head><title>R: Basic graphic utilities for visualization of genomic data.</title>
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<h1> Basic graphic utilities for visualization of genomic data.
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</div><h2>Documentation for package ‘biovizBase’ version 1.26.0</h2>
<ul><li><a href="../DESCRIPTION">DESCRIPTION file</a>.</li>
<li><a href="../doc/index.html">User guides, package vignettes and other documentation.</a></li>
<li><a href="../NEWS">Package NEWS</a>.</li>
</ul>
<h2>Help Pages</h2>
<table width="100%">
<tr><td style="width: 25%;"><a href="biovizBase-package.html">biovizBase-package</a></td>
<td>biovizBase is a package which provides utilities and color scheme...</td></tr>
<tr><td style="width: 25%;"><a href="addStepping-method.html">addStepping</a></td>
<td>Adding disjoint levels to a GenomicRanges object</td></tr>
<tr><td style="width: 25%;"><a href="addStepping-method.html">addStepping-method</a></td>
<td>Adding disjoint levels to a GenomicRanges object</td></tr>
<tr><td style="width: 25%;"><a href="biovizBase-package.html">biovizBase</a></td>
<td>biovizBase is a package which provides utilities and color scheme...</td></tr>
<tr><td style="width: 25%;"><a href="colorBlindSafePal.html">blind.pal.info</a></td>
<td>Color blind safe palette generator</td></tr>
<tr><td style="width: 25%;"><a href="colorBlindSafePal.html">brewer.pal.blind.info</a></td>
<td>Color blind safe palette generator</td></tr>
<tr><td style="width: 25%;"><a href="colorBlindSafePal.html">colorBlindSafePal</a></td>
<td>Color blind safe palette generator</td></tr>
<tr><td style="width: 25%;"><a href="containLetters.html">containLetters</a></td>
<td>Checking if string contains letters or not</td></tr>
<tr><td style="width: 25%;"><a href="CRC.html">CRC</a></td>
<td>CRC</td></tr>
<tr><td style="width: 25%;"><a href="CRC.html">crc.gr</a></td>
<td>CRC</td></tr>
<tr><td style="width: 25%;"><a href="crc1.GeRL.html">crc1.GeRL</a></td>
<td>crc1.GeRL</td></tr>
<tr><td style="width: 25%;"><a href="crunch-method.html">crunch</a></td>
<td>Fetching GRanges from various data source</td></tr>
<tr><td style="width: 25%;"><a href="crunch-method.html">crunch-method</a></td>
<td>Fetching GRanges from various data source</td></tr>
<tr><td style="width: 25%;"><a href="darned_hg19_subset500.html">darned_hg19_subset500</a></td>
<td>Subset of RNA editing sites in hg19...</td></tr>
<tr><td style="width: 25%;"><a href="colorBlindSafePal.html">dichromat.pal.blind.info</a></td>
<td>Color blind safe palette generator</td></tr>
<tr><td style="width: 25%;"><a href="estimateCoverage-method.html">estimateCoverage</a></td>
<td>Estimation of Coverage</td></tr>
<tr><td style="width: 25%;"><a href="estimateCoverage-method.html">estimateCoverage-method</a></td>
<td>Estimation of Coverage</td></tr>
<tr><td style="width: 25%;"><a href="flatGrl.html">flatGrl</a></td>
<td>Transform GRangesList to GRanges</td></tr>
<tr><td style="width: 25%;"><a href="GCcontent.html">GCcontent</a></td>
<td>GC content computation for BSgenome</td></tr>
<tr><td style="width: 25%;"><a href="colorBlindSafePal.html">genBlindPalInfo</a></td>
<td>Color blind safe palette generator</td></tr>
<tr><td style="width: 25%;"><a href="colorBlindSafePal.html">genBrewerBlindPalInfo</a></td>
<td>Color blind safe palette generator</td></tr>
<tr><td style="width: 25%;"><a href="colorBlindSafePal.html">genDichromatPalInfo</a></td>
<td>Color blind safe palette generator</td></tr>
<tr><td style="width: 25%;"><a href="genesymbol.html">genesymbol</a></td>
<td>Gene symbols with position...</td></tr>
<tr><td style="width: 25%;"><a href="getBioColor.html">getBioColor</a></td>
<td>Color scheme getter for biological data</td></tr>
<tr><td style="width: 25%;"><a href="getFormalNames.html">getFormalNames</a></td>
<td>Get formals from functions</td></tr>
<tr><td style="width: 25%;"><a href="getGaps.html">getGaps</a></td>
<td>get gaps for a stepping transformed GRanges object</td></tr>
<tr><td style="width: 25%;"><a href="getGaps.html">getGaps-method</a></td>
<td>get gaps for a stepping transformed GRanges object</td></tr>
<tr><td style="width: 25%;"><a href="getIdeoGR.html">getIdeoGR</a></td>
<td>Get ideogram information</td></tr>
<tr><td style="width: 25%;"><a href="getIdeogram.html">getIdeogram</a></td>
<td>Get ideogram.</td></tr>
<tr><td style="width: 25%;"><a href="getScale.html">getScale</a></td>
<td>Get scale information from a GRanges</td></tr>
<tr><td style="width: 25%;"><a href="labs.html">getXLab</a></td>
<td>parse x and y label information from a specific object</td></tr>
<tr><td style="width: 25%;"><a href="labs.html">getXLab-method</a></td>
<td>parse x and y label information from a specific object</td></tr>
<tr><td style="width: 25%;"><a href="scale.html">getXScale</a></td>
<td>get x scale breaks and labels</td></tr>
<tr><td style="width: 25%;"><a href="scale.html">getXScale-method</a></td>
<td>get x scale breaks and labels</td></tr>
<tr><td style="width: 25%;"><a href="labs.html">getYLab</a></td>
<td>parse x and y label information from a specific object</td></tr>
<tr><td style="width: 25%;"><a href="labs.html">getYLab-method</a></td>
<td>parse x and y label information from a specific object</td></tr>
<tr><td style="width: 25%;"><a href="hg19Ideogram.html">hg19Ideogram</a></td>
<td>Hg19 ideogram without cytoband information...</td></tr>
<tr><td style="width: 25%;"><a href="hg19IdeogramCyto.html">hg19IdeogramCyto</a></td>
<td>Hg19 ideogram with cytoband information...</td></tr>
<tr><td style="width: 25%;"><a href="CRC.html">hg19sub</a></td>
<td>CRC</td></tr>
<tr><td style="width: 25%;"><a href="ideo.html">ideo</a></td>
<td>ideogram without cytoband information</td></tr>
<tr><td style="width: 25%;"><a href="ideoCyto.html">ideoCyto</a></td>
<td>ideogram with cytoband information</td></tr>
<tr><td style="width: 25%;"><a href="isIdeogram.html">isIdeogram</a></td>
<td>Ideogram checking</td></tr>
<tr><td style="width: 25%;"><a href="isMatchedWithModel.html">isJunctionRead</a></td>
<td>Utils for Splicing Summary</td></tr>
<tr><td style="width: 25%;"><a href="isMatchedWithModel.html">isMatchedWithModel</a></td>
<td>Utils for Splicing Summary</td></tr>
<tr><td style="width: 25%;"><a href="isSimpleIdeogram.html">isSimpleIdeogram</a></td>
<td>Simple ideogram checking</td></tr>
<tr><td style="width: 25%;"><a href="transform.html">is_coord_genome</a></td>
<td>Transform GRanges to different coordinates and layout</td></tr>
<tr><td style="width: 25%;"><a href="shrinkageFun-method.html">is_coord_truncate_gaps</a></td>
<td>Shrinkage function</td></tr>
<tr><td style="width: 25%;"><a href="maxGap-method.html">maxGap</a></td>
<td>Estimated max gaps</td></tr>
<tr><td style="width: 25%;"><a href="maxGap-method.html">maxGap-method</a></td>
<td>Estimated max gaps</td></tr>
<tr><td style="width: 25%;"><a href="mold-method.html">mold</a></td>
<td>mold data into data.frame</td></tr>
<tr><td style="width: 25%;"><a href="mold-method.html">mold-method</a></td>
<td>mold data into data.frame</td></tr>
<tr><td style="width: 25%;"><a href="CRC.html">mut.gr</a></td>
<td>CRC</td></tr>
<tr><td style="width: 25%;"><a href="aes-utils.html">parseArgsForAes</a></td>
<td>Utils for parsing (un)evaluated arguments</td></tr>
<tr><td style="width: 25%;"><a href="aes-utils.html">parseArgsForNonAes</a></td>
<td>Utils for parsing (un)evaluated arguments</td></tr>
<tr><td style="width: 25%;"><a href="pileupAsGRanges.html">pileupAsGRanges</a></td>
<td>Summarize reads for certain region</td></tr>
<tr><td style="width: 25%;"><a href="pileupGRangesAsVariantTable.html">pileupGRangesAsVariantTable</a></td>
<td>Mismatch summary</td></tr>
<tr><td style="width: 25%;"><a href="plotColorLegend.html">plotColorLegend</a></td>
<td>Show colors</td></tr>
<tr><td style="width: 25%;"><a href="showColor.html">showColor</a></td>
<td>Show colors</td></tr>
<tr><td style="width: 25%;"><a href="shrinkageFun-method.html">shrinkageFun</a></td>
<td>Shrinkage function</td></tr>
<tr><td style="width: 25%;"><a href="shrinkageFun-method.html">shrinkageFun-method</a></td>
<td>Shrinkage function</td></tr>
<tr><td style="width: 25%;"><a href="splitByFacets-method.html">splitByFacets</a></td>
<td>split a GRanges by formula</td></tr>
<tr><td style="width: 25%;"><a href="splitByFacets-method.html">splitByFacets-method</a></td>
<td>split a GRanges by formula</td></tr>
<tr><td style="width: 25%;"><a href="strip_formula_dots.html">strip_formula_dots</a></td>
<td>strip dots around a formula variables</td></tr>
<tr><td style="width: 25%;"><a href="subsetArgsByFormals.html">subsetArgsByFormals</a></td>
<td>Subset list of arguments by functions</td></tr>
<tr><td style="width: 25%;"><a href="transform.html">transformDfToGr</a></td>
<td>Transform GRanges to different coordinates and layout</td></tr>
<tr><td style="width: 25%;"><a href="transformGRangesForEvenSpace.html">transformGRangesForEvenSpace</a></td>
<td>Transform GRanges with New Coordinates</td></tr>
<tr><td style="width: 25%;"><a href="transform.html">transformToArch</a></td>
<td>Transform GRanges to different coordinates and layout</td></tr>
<tr><td style="width: 25%;"><a href="transform.html">transformToArch-method</a></td>
<td>Transform GRanges to different coordinates and layout</td></tr>
<tr><td style="width: 25%;"><a href="transform.html">transformToBarInCircle</a></td>
<td>Transform GRanges to different coordinates and layout</td></tr>
<tr><td style="width: 25%;"><a href="transform.html">transformToCircle</a></td>
<td>Transform GRanges to different coordinates and layout</td></tr>
<tr><td style="width: 25%;"><a href="transform.html">transformToDf</a></td>
<td>Transform GRanges to different coordinates and layout</td></tr>
<tr><td style="width: 25%;"><a href="transform.html">transformToDf-method</a></td>
<td>Transform GRanges to different coordinates and layout</td></tr>
<tr><td style="width: 25%;"><a href="transform.html">transformToGenome</a></td>
<td>Transform GRanges to different coordinates and layout</td></tr>
<tr><td style="width: 25%;"><a href="transform.html">transformToGenome-method</a></td>
<td>Transform GRanges to different coordinates and layout</td></tr>
<tr><td style="width: 25%;"><a href="transform.html">transformToLinkInCircle</a></td>
<td>Transform GRanges to different coordinates and layout</td></tr>
<tr><td style="width: 25%;"><a href="transform.html">transformToRectInCircle</a></td>
<td>Transform GRanges to different coordinates and layout</td></tr>
<tr><td style="width: 25%;"><a href="transform.html">transformToSegInCircle</a></td>
<td>Transform GRanges to different coordinates and layout</td></tr>
</table>
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