| perturbPlot2d {directPA} | R Documentation |
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)