LandscapePlot

A (non-empty) numeric matrix with trait values

Data

A (non-empty)factor vector indicating the group membership of each row in Data. If there is only a single group present in Data then Groups=NULL (default).

Groups

Logical controlling whether to output the results as a .pdf or a .jpeg. The default (PDF=FALSE) will produce a .jpeg. The file size for .pdf output can be large.

Logical controlling whether to output a .pdf naming the peaks according to the columns they represent. The defaul is FALSE.

LocPlot

An optional numeric vector setting the control parameters for persp. control[1] = theta, control[2] = r, control[3] = phi

control

This function plots a three-dimensional landscape of measured traits. The peak heights are relative with respect to the input data. The width of each peak is controlled by the argument sigma and has only an aesthetic purpose. The 3D image is generated using the <code>drawScene</code> and <code>surfaceTriangles</code> .

Code to support a systems biology research program from inception through publication.  The methods focus on dimension reduction approaches to detect patterns in complex, multivariate experimental data and places an emphasis on informative visualizations.  The goal for this project is to create a package that will evolve over time, thereby remaining relevant and reflective of current methods and techniques.  As a result, we encourage suggested additions to the package, both methodological and graphical.

Samuel V Scarpino

multiDimBio

Multivariate Analysis and Visualization for Biological Data

LandscapePlot function

<dl> <dt>Data</dt>
<dd>A (non-empty) numeric matrix with trait values</dd> <dt>Groups</dt>
<dd>A (non-empty)factor vector indicating the group membership of each row in Data. If there is only a single group present in Data then Groups=NULL (default).</dd> <dt>PDF</dt>
<dd>Logical controlling whether to output the results as a .pdf or a .jpeg. The default (PDF=FALSE) will produce a .jpeg. The file size for .pdf output can be large.</dd> <dt>LocPlot</dt>
<dd>Logical controlling whether to output a .pdf naming the peaks according to the columns they represent. The defaul is FALSE.</dd>	<dt>control</dt>
<dd>An optional numeric vector setting the control parameters for persp. control[1] = theta, control[2] = r, control[3] = phi</dd></dl>

Arguments

A function to visualize the Functional Landscape of measured traits — LandscapePlot

<dl>

 <dt>Data</dt>
<dd>A (non-empty) numeric matrix with trait values</dd>

 <dt>Groups</dt>
<dd>A (non-empty)factor vector indicating the group membership of each row in Data. If there is only a single group present in Data then Groups=NULL (default).</dd>

 <dt>PDF</dt>
<dd>Logical controlling whether to output the results as a .pdf or a .jpeg. The default (PDF=FALSE) will produce a .jpeg. The file size for .pdf output can be large.</dd>

 <dt>LocPlot</dt>
<dd>Logical controlling whether to output a .pdf naming the peaks according to the columns they represent. The defaul is FALSE.</dd>

	<dt>control</dt>
<dd>An optional numeric vector setting the control parameters for persp. control[1] = theta, control[2] = r, control[3] = phi</dd>

</dl>

LandscapePlot: A function to visualize the Functional Landscape of measured traits

Description

Usage

Value

Arguments

Examples