RectangleOverlay-class

drawOverlay,RectangleOverlay-method

classes

Genomic data analyses requires integrated visualization of known genomic information and new experimental data.  GenomeGraphs uses the biomaRt package to perform live annotation queries to Ensembl and translates this to e.g. gene/transcript structures in viewports of the grid graphics package. This results in genomic information plotted together with your data.  Another strength of GenomeGraphs is to plot different data types such as array CGH, gene expression, sequencing and other data, together in one plot using the same genome coordinate system.

Steffen Durinck

GenomeGraphs

Plotting genomic information from Ensembl

RectangleOverlay-class function

Objects can be created by calls of the form makeRectangleOverlay (<code><a rd-options="" href="/link/makeRectangleOverlay?package=GenomeGraphs&version=1.32.0" data-mini-rdoc="GenomeGraphs::makeRectangleOverlay">makeRectangleOverlay</a></code>).

Objects from the Class

<dl>
    <dt><code>start</code>:</dt><dd>Object of class <code>"numeric"</code> ~~ </dd> <dt><code>end</code>:</dt><dd>Object of class <code>"numeric"</code> ~~ </dd> <dt><code>region</code>:</dt><dd>Object of class <code>"numericOrNull"</code> ~~ </dd> <dt><code>coords</code>:</dt><dd>Object of class <code>"character"</code> ~~ </dd> <dt><code>dp</code>:</dt><dd>Object of class <code>"DisplayPars"</code> ~~ </dd> </dl> 

Slots

Class <code>"Overlay"</code>, directly.
  Class <code>"gdObject"</code>, by class "Overlay", distance 2.

Extends

<dl>
    <dt>drawOverlay</dt><dd><code>signature(obj = "RectangleOverlay")</code>: ... </dd> </dl> 

RectangleOverlay-class: Class "RectangleOverlay"

Description

Arguments

Objects from the Class

Slots

Extends

Methods

Examples