347 lines
17 KiB
HTML
347 lines
17 KiB
HTML
<!DOCTYPE html>
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<html>
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<head><title>R: Circular Visualization</title>
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<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
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<meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes" />
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<link rel="stylesheet" type="text/css" href="R.css" />
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</head><body><div class="container">
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<h1> Circular Visualization
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<img class="toplogo" src="../../../doc/html/Rlogo.svg" alt="[R logo]" />
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</h1>
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<hr/>
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<div style="text-align: center;">
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<a href="../../../doc/html/packages.html"><img class="arrow" src="../../../doc/html/left.jpg" alt="[Up]" /></a>
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<a href="../../../doc/html/index.html"><img class="arrow" src="../../../doc/html/up.jpg" alt="[Top]" /></a>
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</div><h2>Documentation for package ‘circlize’ version 0.4.16</h2>
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<ul><li><a href="../DESCRIPTION">DESCRIPTION file</a>.</li>
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<li><a href="../doc/index.html">User guides, package vignettes and other documentation.</a></li>
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<li><a href="../demo">Code demos</a>. Use <a href="../../utils/help/demo">demo()</a> to run them.</li>
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<li><a href="../NEWS">Package NEWS</a>.</li>
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</ul>
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<h2>Help Pages</h2>
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<p style="text-align: center;">
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<a href="# "> </a>
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<a href="#A">A</a>
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<a href="#C">C</a>
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<a href="#D">D</a>
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<a href="#F">F</a>
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<a href="#G">G</a>
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<a href="#H">H</a>
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<a href="#I">I</a>
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<a href="#M">M</a>
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<a href="#N">N</a>
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<a href="#P">P</a>
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<a href="#R">R</a>
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<a href="#S">S</a>
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<a href="#U">U</a>
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<a href="#misc">misc</a>
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</p>
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<table style="width: 100%;">
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<tr><td style="width: 25%;"><a href="circlize-package.html">circlize-package</a></td>
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<td>Circular visualization in R</td></tr>
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</table>
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<h2><a id="A">-- A --</a></h2>
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<table style="width: 100%;">
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<tr><td style="width: 25%;"><a href="add_transparency.html">add_transparency</a></td>
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<td>Add transparency to colors</td></tr>
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<tr><td style="width: 25%;"><a href="adjacencyList2Matrix.html">adjacencyList2Matrix</a></td>
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<td>Convert adjacency list to an adjacency matrix</td></tr>
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<tr><td style="width: 25%;"><a href="adjacencyMatrix2List.html">adjacencyMatrix2List</a></td>
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<td>Convert adjacency matrix to an adjacency list</td></tr>
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<tr><td style="width: 25%;"><a href="arrange_links_evenly.html">arrange_links_evenly</a></td>
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<td>Arrange links evenly on each sector</td></tr>
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</table>
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<h2><a id="C">-- C --</a></h2>
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<table style="width: 100%;">
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<tr><td style="width: 25%;"><a href="calc_gap.html">calc_gap</a></td>
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<td>Calculate gaps to make two Chord diagrams in the same scale</td></tr>
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<tr><td style="width: 25%;"><a href="CELL_META.html">CELL_META</a></td>
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<td>Easy way to get meta data in the current cell</td></tr>
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<tr><td style="width: 25%;"><a href="chordDiagram.html">chordDiagram</a></td>
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<td>Plot Chord Diagram</td></tr>
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<tr><td style="width: 25%;"><a href="chordDiagramFromDataFrame.html">chordDiagramFromDataFrame</a></td>
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<td>Plot Chord Diagram from a data frame</td></tr>
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<tr><td style="width: 25%;"><a href="chordDiagramFromMatrix.html">chordDiagramFromMatrix</a></td>
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<td>Plot Chord Diagram from an adjacency matrix</td></tr>
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<tr><td style="width: 25%;"><a href="circlize.html">circlize</a></td>
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<td>Convert to polar coordinate system</td></tr>
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<tr><td style="width: 25%;"><a href="circos.arrow.html">circos.arrow</a></td>
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<td>Draw arrow which is paralle to the circle</td></tr>
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<tr><td style="width: 25%;"><a href="circos.axis.html">circos.axis</a></td>
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<td>Draw x-axis</td></tr>
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<tr><td style="width: 25%;"><a href="circos.barplot.html">circos.barplot</a></td>
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<td>Draw barplots</td></tr>
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<tr><td style="width: 25%;"><a href="circos.boxplot.html">circos.boxplot</a></td>
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<td>Draw boxplots</td></tr>
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<tr><td style="width: 25%;"><a href="circos.clear.html">circos.clear</a></td>
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<td>Reset the circular layout parameters</td></tr>
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<tr><td style="width: 25%;"><a href="circos.connect.html">circos.connect</a></td>
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<td>Draw connecting lines/ribons between two sets of points</td></tr>
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<tr><td style="width: 25%;"><a href="circos.dendrogram.html">circos.dendrogram</a></td>
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<td>Add circular dendrograms</td></tr>
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<tr><td style="width: 25%;"><a href="circos.genomicAxis.html">circos.genomicAxis</a></td>
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<td>Add genomic axes</td></tr>
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<tr><td style="width: 25%;"><a href="circos.genomicDensity.html">circos.genomicDensity</a></td>
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<td>Calculate and add genomic density track</td></tr>
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<tr><td style="width: 25%;"><a href="circos.genomicHeatmap.html">circos.genomicHeatmap</a></td>
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<td>Add heatmaps for selected regions</td></tr>
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<tr><td style="width: 25%;"><a href="circos.genomicIdeogram.html">circos.genomicIdeogram</a></td>
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<td>Add an ideogram track</td></tr>
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<tr><td style="width: 25%;"><a href="circos.genomicInitialize.html">circos.genomicInitialize</a></td>
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<td>Initialize circular plot with any genomic data</td></tr>
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<tr><td style="width: 25%;"><a href="circos.genomicLabels.html">circos.genomicLabels</a></td>
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<td>Add labels to specified genomic regions</td></tr>
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<tr><td style="width: 25%;"><a href="circos.genomicLines.html">circos.genomicLines</a></td>
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<td>Add lines to a plotting region, specifically for genomic graphics</td></tr>
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<tr><td style="width: 25%;"><a href="circos.genomicLink.html">circos.genomicLink</a></td>
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<td>Add links from two sets of genomic positions</td></tr>
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<tr><td style="width: 25%;"><a href="circos.genomicPoints.html">circos.genomicPoints</a></td>
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<td>Add points to a plotting region, specifically for genomic graphics</td></tr>
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<tr><td style="width: 25%;"><a href="circos.genomicPosTransformLines.html">circos.genomicPosTransformLines</a></td>
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<td>Add genomic position transformation lines between tracks</td></tr>
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<tr><td style="width: 25%;"><a href="circos.genomicRainfall.html">circos.genomicRainfall</a></td>
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<td>Genomic rainfall plot</td></tr>
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<tr><td style="width: 25%;"><a href="circos.genomicRect.html">circos.genomicRect</a></td>
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<td>Draw rectangle-like grid, specifically for genomic graphics</td></tr>
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<tr><td style="width: 25%;"><a href="circos.genomicText.html">circos.genomicText</a></td>
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<td>Draw text in a cell, specifically for genomic graphics</td></tr>
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<tr><td style="width: 25%;"><a href="circos.genomicTrack.html">circos.genomicTrack</a></td>
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<td>Create a track for genomic graphics</td></tr>
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<tr><td style="width: 25%;"><a href="circos.genomicTrackPlotRegion.html">circos.genomicTrackPlotRegion</a></td>
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<td>Create a track for genomic graphics</td></tr>
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<tr><td style="width: 25%;"><a href="circos.heatmap.html">circos.heatmap</a></td>
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<td>Make circular heatmaps</td></tr>
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<tr><td style="width: 25%;"><a href="circos.heatmap.initialize.html">circos.heatmap.initialize</a></td>
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<td>Initialize circular heatmaps</td></tr>
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<tr><td style="width: 25%;"><a href="circos.heatmap.link.html">circos.heatmap.link</a></td>
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<td>Draw a link between two matrix rows in the circular heatmap</td></tr>
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<tr><td style="width: 25%;"><a href="circos.info.html">circos.info</a></td>
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<td>Get information of the circular plot</td></tr>
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<tr><td style="width: 25%;"><a href="circos.initialize.html">circos.initialize</a></td>
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<td>Initialize the circular layout</td></tr>
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<tr><td style="width: 25%;"><a href="circos.initializeCircularGenome.html">circos.initializeCircularGenome</a></td>
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<td>Initialize a layout for circular genome</td></tr>
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<tr><td style="width: 25%;"><a href="circos.initializeWithIdeogram.html">circos.initializeWithIdeogram</a></td>
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<td>Initialize the circular layout with an ideogram</td></tr>
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<tr><td style="width: 25%;"><a href="circos.labels.html">circos.labels</a></td>
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<td>Add a label track</td></tr>
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<tr><td style="width: 25%;"><a href="circos.lines.html">circos.lines</a></td>
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<td>Add lines to the plotting region</td></tr>
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<tr><td style="width: 25%;"><a href="circos.link.html">circos.link</a></td>
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<td>Draw links between points or/and intervals</td></tr>
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<tr><td style="width: 25%;"><a href="circos.nested.html">circos.nested</a></td>
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<td>Nested zooming with two circular plots</td></tr>
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<tr><td style="width: 25%;"><a href="circos.par.html">circos.par</a></td>
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<td>Parameters for the circular layout</td></tr>
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<tr><td style="width: 25%;"><a href="circos.points.html">circos.points</a></td>
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<td>Add points to a plotting region</td></tr>
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<tr><td style="width: 25%;"><a href="circos.polygon.html">circos.polygon</a></td>
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<td>Draw polygon</td></tr>
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<tr><td style="width: 25%;"><a href="circos.raster.html">circos.raster</a></td>
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<td>Add raster images</td></tr>
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<tr><td style="width: 25%;"><a href="circos.rect.html">circos.rect</a></td>
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<td>Draw rectangle-like grid</td></tr>
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<tr><td style="width: 25%;"><a href="circos.segments.html">circos.segments</a></td>
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<td>Draw segments through pairwise of points</td></tr>
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<tr><td style="width: 25%;"><a href="circos.text.html">circos.text</a></td>
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<td>Draw text in a cell</td></tr>
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<tr><td style="width: 25%;"><a href="circos.track.html">circos.track</a></td>
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<td>Create plotting regions for a whole track</td></tr>
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<tr><td style="width: 25%;"><a href="circos.trackHist.html">circos.trackHist</a></td>
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<td>Draw histogram in cells among a whole track</td></tr>
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<tr><td style="width: 25%;"><a href="circos.trackLines.html">circos.trackLines</a></td>
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<td>Add lines to the plotting regions in a same track</td></tr>
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<tr><td style="width: 25%;"><a href="circos.trackPlotRegion.html">circos.trackPlotRegion</a></td>
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<td>Create plotting regions for a whole track</td></tr>
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<tr><td style="width: 25%;"><a href="circos.trackPoints.html">circos.trackPoints</a></td>
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<td>Add points to the plotting regions in a same track</td></tr>
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<tr><td style="width: 25%;"><a href="circos.trackText.html">circos.trackText</a></td>
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<td>Draw text in cells among the whole track</td></tr>
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<tr><td style="width: 25%;"><a href="circos.triangle.html">circos.triangle</a></td>
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<td>Draw triangles</td></tr>
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<tr><td style="width: 25%;"><a href="circos.update.html">circos.update</a></td>
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<td>Create plotting regions for a whole track</td></tr>
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<tr><td style="width: 25%;"><a href="circos.updatePlotRegion.html">circos.updatePlotRegion</a></td>
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<td>Update the plotting region in an existed cell</td></tr>
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<tr><td style="width: 25%;"><a href="circos.violin.html">circos.violin</a></td>
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<td>Draw violin plots</td></tr>
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<tr><td style="width: 25%;"><a href="circos.xaxis.html">circos.xaxis</a></td>
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<td>Draw x-axis</td></tr>
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<tr><td style="width: 25%;"><a href="circos.yaxis.html">circos.yaxis</a></td>
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<td>Draw y-axis</td></tr>
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<tr><td style="width: 25%;"><a href="cm_h.html">cm_h</a></td>
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<td>Convert units</td></tr>
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<tr><td style="width: 25%;"><a href="cm_x.html">cm_x</a></td>
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<td>Convert unit on x direction in data coordinate</td></tr>
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<tr><td style="width: 25%;"><a href="cm_y.html">cm_y</a></td>
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<td>Convert unit on y direction in data coordinate</td></tr>
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<tr><td style="width: 25%;"><a href="col2value.html">col2value</a></td>
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<td>Transform back from colors to values</td></tr>
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<tr><td style="width: 25%;"><a href="colorRamp2.html">colorRamp2</a></td>
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<td>Color interpolation</td></tr>
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<tr><td style="width: 25%;"><a href="convert_height.html">convert_height</a></td>
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<td>Convert units</td></tr>
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<tr><td style="width: 25%;"><a href="convert_length.html">convert_length</a></td>
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<td>Convert units</td></tr>
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<tr><td style="width: 25%;"><a href="convert_x.html">convert_x</a></td>
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<td>Convert unit on x direction in data coordinate</td></tr>
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<tr><td style="width: 25%;"><a href="convert_y.html">convert_y</a></td>
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<td>Convert unit on y direction in data coordinate</td></tr>
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<tr><td style="width: 25%;"><a href="cytoband.col.html">cytoband.col</a></td>
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<td>Assign colors to cytogenetic band (hg19) according to the Giemsa stain results</td></tr>
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</table>
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<h2><a id="D">-- D --</a></h2>
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<table style="width: 100%;">
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<tr><td style="width: 25%;"><a href="degree.html">degree</a></td>
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<td>Mark the value as a degree value</td></tr>
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<tr><td style="width: 25%;"><a href="draw.sector.html">draw.sector</a></td>
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<td>Draw sectors or rings in a circle</td></tr>
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</table>
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<h2><a id="F">-- F --</a></h2>
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<table style="width: 100%;">
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<tr><td style="width: 25%;"><a href="fontsize.html">fontsize</a></td>
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<td>Convert fontsize to cex</td></tr>
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</table>
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<h2><a id="G">-- G --</a></h2>
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<table style="width: 100%;">
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<tr><td style="width: 25%;"><a href="generateRandomBed.html">generateRandomBed</a></td>
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<td>Generate random genomic data</td></tr>
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<tr><td style="width: 25%;"><a href="genomicDensity.html">genomicDensity</a></td>
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<td>Calculate genomic region density</td></tr>
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<tr><td style="width: 25%;"><a href="get.all.sector.index.html">get.all.sector.index</a></td>
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<td>Get index for all sectors</td></tr>
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<tr><td style="width: 25%;"><a href="get.all.track.index.html">get.all.track.index</a></td>
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<td>Get index for all tracks</td></tr>
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<tr><td style="width: 25%;"><a href="get.cell.meta.data.html">get.cell.meta.data</a></td>
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<td>Get the meta data of a cell</td></tr>
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<tr><td style="width: 25%;"><a href="get.current.chromosome.html">get.current.chromosome</a></td>
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<td>Get current chromosome name</td></tr>
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<tr><td style="width: 25%;"><a href="get.current.sector.index.html">get.current.sector.index</a></td>
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<td>Get current sector index</td></tr>
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<tr><td style="width: 25%;"><a href="get.current.track.index.html">get.current.track.index</a></td>
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<td>Get current track index</td></tr>
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<tr><td style="width: 25%;"><a href="getI.html">getI</a></td>
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<td>Which data that 'panel.fun' is using</td></tr>
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<tr><td style="width: 25%;"><a href="get_most_inside_radius.html">get_most_inside_radius</a></td>
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<td>Get the inside radius of the most inner track</td></tr>
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</table>
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<h2><a id="H">-- H --</a></h2>
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<table style="width: 100%;">
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<tr><td style="width: 25%;"><a href="highlight.chromosome.html">highlight.chromosome</a></td>
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<td>Highlight chromosomes</td></tr>
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<tr><td style="width: 25%;"><a href="highlight.sector.html">highlight.sector</a></td>
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<td>Highlight sectors and tracks</td></tr>
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</table>
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<h2><a id="I">-- I --</a></h2>
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<table style="width: 100%;">
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<tr><td style="width: 25%;"><a href="inches_h.html">inches_h</a></td>
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<td>Convert units</td></tr>
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<tr><td style="width: 25%;"><a href="inches_x.html">inches_x</a></td>
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<td>Convert unit on x direction in data coordinate</td></tr>
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<tr><td style="width: 25%;"><a href="inches_y.html">inches_y</a></td>
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<td>Convert unit on y direction in data coordinate</td></tr>
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<tr><td style="width: 25%;"><a href="inch_h.html">inch_h</a></td>
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<td>Convert units</td></tr>
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<tr><td style="width: 25%;"><a href="inch_x.html">inch_x</a></td>
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<td>Convert unit on x direction in data coordinate</td></tr>
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<tr><td style="width: 25%;"><a href="inch_y.html">inch_y</a></td>
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<td>Convert unit on y direction in data coordinate</td></tr>
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</table>
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<h2><a id="M">-- M --</a></h2>
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<table style="width: 100%;">
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<tr><td style="width: 25%;"><a href="mm_h.html">mm_h</a></td>
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<td>Convert units</td></tr>
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<tr><td style="width: 25%;"><a href="mm_x.html">mm_x</a></td>
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<td>Convert unit on x direction in data coordinate</td></tr>
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<tr><td style="width: 25%;"><a href="mm_y.html">mm_y</a></td>
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<td>Convert unit on y direction in data coordinate</td></tr>
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</table>
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<h2><a id="N">-- N --</a></h2>
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<table style="width: 100%;">
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<tr><td style="width: 25%;"><a href="names.CELL_META.html">names.CELL_META</a></td>
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<td>Names of all meta data in the current cell</td></tr>
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</table>
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<h2><a id="P">-- P --</a></h2>
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<table style="width: 100%;">
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<tr><td style="width: 25%;"><a href="posTransform.default.html">posTransform.default</a></td>
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<td>Genomic position transformation function</td></tr>
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<tr><td style="width: 25%;"><a href="posTransform.text.html">posTransform.text</a></td>
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<td>Genomic position transformation function specifically for text</td></tr>
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<tr><td style="width: 25%;"><a href="print.CELL_META.html">print.CELL_META</a></td>
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<td>Print CELL_META</td></tr>
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</table>
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<h2><a id="R">-- R --</a></h2>
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<table style="width: 100%;">
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<tr><td style="width: 25%;"><a href="rainfallTransform.html">rainfallTransform</a></td>
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<td>Calculate inter-distance of genomic regions</td></tr>
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<tr><td style="width: 25%;"><a href="rand_color.html">rand_color</a></td>
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<td>Generate random colors</td></tr>
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<tr><td style="width: 25%;"><a href="read.chromInfo.html">read.chromInfo</a></td>
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<td>Read/parse chromInfo data from a data frame/file/UCSC database</td></tr>
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<tr><td style="width: 25%;"><a href="read.cytoband.html">read.cytoband</a></td>
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<td>Read/parse cytoband data from a data frame/file/UCSC database</td></tr>
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<tr><td style="width: 25%;"><a href="reverse.circlize.html">reverse.circlize</a></td>
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<td>Convert to data coordinate system</td></tr>
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</table>
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<h2><a id="S">-- S --</a></h2>
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<table style="width: 100%;">
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<tr><td style="width: 25%;"><a href="set.current.cell.html">set.current.cell</a></td>
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<td>Set flag to current cell</td></tr>
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<tr><td style="width: 25%;"><a href="set_track_gap.html">set_track_gap</a></td>
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<td>Set gaps between tracks</td></tr>
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<tr><td style="width: 25%;"><a href="show.index.html">show.index</a></td>
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<td>Label the sector index and the track index on each cell</td></tr>
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<tr><td style="width: 25%;"><a href="smartAlign.html">smartAlign</a></td>
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<td>Adjust positions of text</td></tr>
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<tr><td style="width: 25%;"><a href="Subset.CELL_META.html">Subset.CELL_META</a></td>
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<td>Easy to way to get meta data in the current cell</td></tr>
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</table>
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<h2><a id="U">-- U --</a></h2>
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<table style="width: 100%;">
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<tr><td style="width: 25%;"><a href="uh.html">uh</a></td>
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<td>Convert units</td></tr>
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<tr><td style="width: 25%;"><a href="ux.html">ux</a></td>
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<td>Convert unit on x direction in data coordinate</td></tr>
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<tr><td style="width: 25%;"><a href="uy.html">uy</a></td>
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<td>Convert unit on y direction in data coordinate</td></tr>
|
|
</table>
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|
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<h2><a id="misc">-- misc --</a></h2>
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|
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<table style="width: 100%;">
|
|
<tr><td style="width: 25%;"><a href="Subset.CELL_META.html">$.CELL_META</a></td>
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<td>Easy to way to get meta data in the current cell</td></tr>
|
|
</table>
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|
</div></body></html>
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