monsterTransitionPCAPlot: Principal Components plot of transformation matrix

In netZoo/netZooR: Unified methods for the inference and analysis of gene regulatory networks

Principal Components plot of transformation matrix

Description

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)

netZoo/netZooR documentation built on Oct. 16, 2024, 10:23 p.m.