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, ...)
Value
a list of coordinates for pathways or kinases
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.