transitionPCAPlot: Principal Components plot of transformation matrix

In QuackenbushLab/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

monsterObj	a monsterAnalysis object resulting from a monster analysis
title	The title of the plot
clusters	A vector indicating the number of clusters to compute
alpha	A vector indicating the level of transparency to be plotted

Value

ggplot2 object for transition matrix PCA

Examples

# data(yeast)
# design <- c(rep(0,20),rep(NA,10),rep(1,20))
# monsterRes <- monster(yeast$exp.cc, design, yeast$motif, nullPerms=100, numMaxCores=4)#' 
data(monsterRes)
# 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)

QuackenbushLab/MONSTER documentation built on Oct. 22, 2020, 8:07 a.m.