Principal Components plot of transformation matrix — monsterTransitionPCAPlot • netZooR

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

Usage

monsterTransitionPCAPlot(
  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))
# yeast$exp.cc[is.na(yeast$exp.cc)] <- mean(as.matrix(yeast$exp.cc),na.rm=TRUE)
# monsterRes <- monster(yeast$exp.cc, design, yeast$motif, nullPerms=100, numMaxCores=4)#' 
data(monsterRes)
# Color the nodes according to cluster membership
clusters <- kmeans(monsterGetTm(monsterRes),3)$cluster 
monsterTransitionPCAPlot(monsterRes, 
title="PCA Plot of Transition - Cell Cycle vs Stress Response", 
clusters=clusters)