perturbPlot2d: Perturbation Plot

In directPA: Direction Analysis for Pathways and Kinases

Perturbation Plot

Description

This function takes in a matrix of test statistics with two columns (2-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.

Usage

perturbPlot2d(Tc, annotation, minSize=5, ...)

Arguments

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

Value

a list of coordinates for pathways or kinases

Examples

# load the phosphoproteomics dataset
data(HEK)

# load the kinase-substrate annoations
data(PhosphoSite)

perturbPlot2d(Tc=HEK, annotation=PhosphoSite.mouse, cex=3)

directPA documentation built on Nov. 17, 2023, 1:08 a.m.