RCircos.Link.Data

A data frame containing paired genomic position data for each row. The content of each row must be in the order of name, start and end position of chromosome A then name, start and end position of chromosome B. This data frame is directly used to draw link lines without extra processing.

datasets

A simple and flexible way to generate Circos 2D track plot images for genomic data visualization is implemented in this package. The types of plots include: heatmap, histogram, lines, scatterplot, tiles and plot items for further decorations include connector, link (lines and ribbons), and text (gene) label. All functions require only R graphics package that comes with R base installation.

Hongen Zhang

RCircos

Circos 2D Track Plot

RCircos.Link.Data function

A data frame with 71 observations on the following 6 variables.<dl class="dl-horizontal">
 <dt><code>Chromosome</code></dt><dd>a factor with levels <code>chr1</code> <code>chr10</code> <code>chr11</code> <code>chr12</code> <code>chr14</code> <code>chr15</code> <code>chr17</code> <code>chr19</code> <code>chr2</code> <code>chr21</code> <code>chr22</code> <code>chr3</code> <code>chr4</code> <code>chr5</code> <code>chr6</code> <code>chr7</code> <code>chr8</code> <code>chr9</code> <code>chrX</code></dd>
 <dt><code>chromStart</code></dt><dd>a numeric vector</dd>
 <dt><code>chromEnd</code></dt><dd>a numeric vector</dd>
 <dt><code>Chromosome.1</code></dt><dd>a factor with levels <code>chr1</code> <code>chr10</code> <code>chr11</code> <code>chr12</code> <code>chr14</code> <code>chr15</code> <code>chr16</code> <code>chr17</code> <code>chr18</code> <code>chr19</code> <code>chr2</code> <code>chr20</code> <code>chr21</code> <code>chr22</code> <code>chr3</code> <code>chr4</code> <code>chr5</code> <code>chr6</code> <code>chr7</code> <code>chr8</code> <code>chr9</code> <code>chrX</code></dd>
 <dt><code>chromStart.1</code></dt><dd>a numeric vector</dd>
 <dt><code>chromEnd.1</code></dt><dd>a numeric vector</dd>
 </dl>

Format

Sample Data for RCircos Link Plot — RCircos.Link.Data

A data frame with 71 observations on the following 6 variables.<dl class='dl-horizontal'>
 <dt><code>Chromosome</code></dt><dd>a factor with levels <code>chr1</code> <code>chr10</code> <code>chr11</code> <code>chr12</code> <code>chr14</code> <code>chr15</code> <code>chr17</code> <code>chr19</code> <code>chr2</code> <code>chr21</code> <code>chr22</code> <code>chr3</code> <code>chr4</code> <code>chr5</code> <code>chr6</code> <code>chr7</code> <code>chr8</code> <code>chr9</code> <code>chrX</code></dd>
 <dt><code>chromStart</code></dt><dd>a numeric vector</dd>
 <dt><code>chromEnd</code></dt><dd>a numeric vector</dd>
 <dt><code>Chromosome.1</code></dt><dd>a factor with levels <code>chr1</code> <code>chr10</code> <code>chr11</code> <code>chr12</code> <code>chr14</code> <code>chr15</code> <code>chr16</code> <code>chr17</code> <code>chr18</code> <code>chr19</code> <code>chr2</code> <code>chr20</code> <code>chr21</code> <code>chr22</code> <code>chr3</code> <code>chr4</code> <code>chr5</code> <code>chr6</code> <code>chr7</code> <code>chr8</code> <code>chr9</code> <code>chrX</code></dd>
 <dt><code>chromStart.1</code></dt><dd>a numeric vector</dd>
 <dt><code>chromEnd.1</code></dt><dd>a numeric vector</dd>
 </dl>

RCircos.Link.Data: Sample Data for RCircos Link Plot

Description

Usage

Arguments

Format