transitionPCAPlot: Principal Components plot of transformation matrix

In dschlauch/MONSTER: Modeling Network State Transitions from Expression and Regulatory data (MONSTER)

Description

This function plots the first two principal components for a transaction matrix

Usage

transitionPCAPlot(monsterObj, title = "PCA Plot of Transition",
  clusters = 1, alpha = 1)

Arguments

title	The title of the plot
clusters	A vector indicating the colors to be plotted for each node
alpha	A vector indicating the level of transparency to be plotted for each node
tm	a transition matrix for a bipartite network

Value

ggplot2 object for transition matrix PCA

Examples

data(yeast)
monsterRes <- monster(yeast$exp.ko,c(rep(1,42),rep(0,49),rep(NA,15)),
    yeast$motif, nullPerms=10, numMaxCores=4)
# Color the nodes according to cluster membership
clusters <- kmeans(slot(monsterRes, 'tm'),3)$cluster 
transitionPCAPlot(monsterRes, 
title="PCA Plot of Transition - Cell Cycle vs Stress Response", 
clusters=clusters)

dschlauch/MONSTER documentation built on May 15, 2019, 2:57 p.m.