pca.plot: Principal Components plot of transformation matrix

In dschlauch/bptools: Bi-partite network analysis tools

Description

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

Usage

pca.plot(tm, title = "PCA Plot of Transition", clusters = 1, alpha = 1)

Arguments

tm	a transition matrix for a bipartite network
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

Examples

data(yeast.panda)
t.matrix <- transformation.matrix(yeast.panda$cell.cycle, yeast.panda$stress.response)
p.values <- runif(ncol(t.matrix))  # Generate a uniform random to simulate p.values
clusters <- kmeans(t.matrix,3)$cluster # Color the nodes according to cluster membership
pca.plot(t.matrix,title="PCA Plot of Transition - Cell Cycle vs Stress Response", clusters=clusters,alpha=p.values)

dschlauch/bptools documentation built on May 15, 2019, 2:58 p.m.