perturbPlot3d

This function takes in a matrix of test statistics with two columns (3-dimensional space) and the 
annotation list such as pathway annotation or kinase-substrate annotation, and visualize the enrichment
of pathways or kinases in direction specific manner.

Direction analysis is a set of tools designed to identify
combinatorial effects of multiple treatments/conditions on pathways
and kinases profiled by microarray, RNA-seq, proteomics, or phosphoproteomics
data. See Yang P et al (2014) <doi:10.1093/bioinformatics/btt616>; and Yang P et al. (2016) <doi:10.1002/pmic.201600068>.

Pengyi Yang

directPA

Direction Analysis for Pathways and Kinases

perturbPlot3d function

<dl><dt>Tc</dt>
<dd>a numeric matrix. The columns are genes or phosphorylation sites and the columns are treatments 
vs control statistics.</dd>
<dt>annotation</dt>
<dd>a list with names correspond to pathways or kinases and elements correspond to genes or
substrates belong to each pathway or kinase, respectively.</dd>
<dt>minSize</dt>
<dd>the size of annotation groups to be considered for calculating enrichment. Groups 
that are smaller than the minSize will be removed from the analysis.</dd>
<dt>...</dt>
<dd>parameters for controling the plot.</dd></dl>

Arguments

Perturbation Plot 3D — perturbPlot3d

<dl>

<dt>Tc</dt>
<dd>a numeric matrix. The columns are genes or phosphorylation sites and the columns are treatments 
vs control statistics.</dd>


<dt>annotation</dt>
<dd>a list with names correspond to pathways or kinases and elements correspond to genes or
substrates belong to each pathway or kinase, respectively.</dd>


<dt>minSize</dt>
<dd>the size of annotation groups to be considered for calculating enrichment. Groups 
that are smaller than the minSize will be removed from the analysis.</dd>


<dt>...</dt>
<dd>parameters for controling the plot.</dd>

</dl>

perturbPlot3d: Perturbation Plot 3D

Description

Usage

Value

Arguments