UCSC.Mouse.GRCm38.CytoBandIdeogram

A data frame containing chromosome name, start and end position, band name, and intensity of Giemsa stains for each cytoband.

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

UCSC.Mouse.GRCm38.CytoBandIdeogram function

A data frame with 403 observations on the following 5 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>chr13</code> <code>chr14</code> <code>chr15</code> <code>chr16</code> <code>chr17</code> <code>chr18</code> <code>chr19</code> <code>chr2</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> <code>chrY</code></dd>
 <dt><code>ChromStart</code></dt><dd>a numeric vector</dd>
 <dt><code>ChromEnd</code></dt><dd>a numeric vector</dd>
 <dt><code>Band</code></dt><dd>a factor with levels <code>qA</code> <code>qA1</code> <code>qA1.1</code> <code>qA1.2</code> <code>qA1.3</code> <code>qA2</code> <code>qA3</code> <code>qA3.1</code> <code>qA3.2</code> <code>qA3.3</code> <code>qA4</code> <code>qA5</code> <code>qA5.1</code> <code>qA5.2</code> <code>qA5.3</code> <code>qA6</code> <code>qA7.1</code> <code>qA7.2</code> <code>qA7.3</code> <code>qB</code> <code>qB1</code> <code>qB1.1</code> <code>qB1.2</code> <code>qB1.3</code> <code>qB2</code> <code>qB2.1</code> <code>qB2.2</code> <code>qB2.3</code> <code>qB3</code> <code>qB3.1</code> <code>qB3.2</code> <code>qB3.3</code> <code>qB4</code> <code>qB5</code> <code>qB5.1</code> <code>qB5.2</code> <code>qB5.3</code> <code>qC</code> <code>qC1</code> <code>qC1.1</code> <code>qC1.2</code> <code>qC1.3</code> <code>qC2</code> <code>qC3</code> <code>qC3.1</code> <code>qC3.2</code> <code>qC3.3</code> <code>qC4</code> <code>qC5</code> <code>qC6</code> <code>qC7</code> <code>qD</code> <code>qD1</code> <code>qD2</code> <code>qD2.1</code> <code>qD2.2</code> <code>qD2.3</code> <code>qD3</code> <code>qE</code> <code>qE1</code> <code>qE1.1</code> <code>qE1.2</code> <code>qE1.3</code> <code>qE2</code> <code>qE2.1</code> <code>qE2.2</code> <code>qE2.3</code> <code>qE3</code> <code>qE3.1</code> <code>qE3.2</code> <code>qE3.3</code> <code>qE4</code> <code>qE5</code> <code>qF</code> <code>qF1</code> <code>qF2</code> <code>qF2.1</code> <code>qF2.2</code> <code>qF2.3</code> <code>qF3</code> <code>qF4</code> <code>qF5</code> <code>qG1</code> <code>qG1.1</code> <code>qG1.2</code> <code>qG1.3</code> <code>qG2</code> <code>qG3</code> <code>qH1</code> <code>qH2</code> <code>qH2.1</code> <code>qH2.2</code> <code>qH2.3</code> <code>qH3</code> <code>qH4</code> <code>qH5</code> <code>qH6</code></dd>
 <dt><code>Stain</code></dt><dd>a factor with levels <code>gneg</code> <code>gpos100</code> <code>gpos33</code> <code>gpos66</code> <code>gpos75</code></dd>
 </dl>

Format

Cytoband Inforamtion for Mouse Chromosome Ideogram — UCSC.Mouse.GRCm38.CytoBandIdeogram

A data frame with 403 observations on the following 5 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>chr13</code> <code>chr14</code> <code>chr15</code> <code>chr16</code> <code>chr17</code> <code>chr18</code> <code>chr19</code> <code>chr2</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> <code>chrY</code></dd>
 <dt><code>ChromStart</code></dt><dd>a numeric vector</dd>
 <dt><code>ChromEnd</code></dt><dd>a numeric vector</dd>
 <dt><code>Band</code></dt><dd>a factor with levels <code>qA</code> <code>qA1</code> <code>qA1.1</code> <code>qA1.2</code> <code>qA1.3</code> <code>qA2</code> <code>qA3</code> <code>qA3.1</code> <code>qA3.2</code> <code>qA3.3</code> <code>qA4</code> <code>qA5</code> <code>qA5.1</code> <code>qA5.2</code> <code>qA5.3</code> <code>qA6</code> <code>qA7.1</code> <code>qA7.2</code> <code>qA7.3</code> <code>qB</code> <code>qB1</code> <code>qB1.1</code> <code>qB1.2</code> <code>qB1.3</code> <code>qB2</code> <code>qB2.1</code> <code>qB2.2</code> <code>qB2.3</code> <code>qB3</code> <code>qB3.1</code> <code>qB3.2</code> <code>qB3.3</code> <code>qB4</code> <code>qB5</code> <code>qB5.1</code> <code>qB5.2</code> <code>qB5.3</code> <code>qC</code> <code>qC1</code> <code>qC1.1</code> <code>qC1.2</code> <code>qC1.3</code> <code>qC2</code> <code>qC3</code> <code>qC3.1</code> <code>qC3.2</code> <code>qC3.3</code> <code>qC4</code> <code>qC5</code> <code>qC6</code> <code>qC7</code> <code>qD</code> <code>qD1</code> <code>qD2</code> <code>qD2.1</code> <code>qD2.2</code> <code>qD2.3</code> <code>qD3</code> <code>qE</code> <code>qE1</code> <code>qE1.1</code> <code>qE1.2</code> <code>qE1.3</code> <code>qE2</code> <code>qE2.1</code> <code>qE2.2</code> <code>qE2.3</code> <code>qE3</code> <code>qE3.1</code> <code>qE3.2</code> <code>qE3.3</code> <code>qE4</code> <code>qE5</code> <code>qF</code> <code>qF1</code> <code>qF2</code> <code>qF2.1</code> <code>qF2.2</code> <code>qF2.3</code> <code>qF3</code> <code>qF4</code> <code>qF5</code> <code>qG1</code> <code>qG1.1</code> <code>qG1.2</code> <code>qG1.3</code> <code>qG2</code> <code>qG3</code> <code>qH1</code> <code>qH2</code> <code>qH2.1</code> <code>qH2.2</code> <code>qH2.3</code> <code>qH3</code> <code>qH4</code> <code>qH5</code> <code>qH6</code></dd>
 <dt><code>Stain</code></dt><dd>a factor with levels <code>gneg</code> <code>gpos100</code> <code>gpos33</code> <code>gpos66</code> <code>gpos75</code></dd>
 </dl>

UCSC.Mouse.GRCm38.CytoBandIdeogram: Cytoband Inforamtion for Mouse Chromosome Ideogram

Description

Usage

Arguments

Format