Plot nodes of the representative tree

Description

This function visualizes the representative tree of the output of the mrs function. For each node of the representative tree, the posterior probability of difference (PMAP) or the effect size is plotted. Each node in the tree is associated to a region of the sample space. All non-terminal nodes have two children nodes obtained by partitiing the parent region with a dyadic cut along a given direction. The numbers under the vertices represent the cutting direction.

Usage

plotTree(ans, type = "prob", group = 1, legend = FALSE, main = "",
  node.size = 5)

Arguments

Note

The package igraph is required.

References

Soriano J. and Ma L. (2014). Multi-resolution two-sample comparison through the divide-merge Markov tree. Preprint. http://arxiv.org/abs/1404.3753

Examples

set.seed(1)
p = 2
n1 = 200
n2 = 200
mu1 = matrix( c(9,9,0,4,-2,-10,3,6,6,-10), nrow = 5, byrow=TRUE)
mu2 = mu1; mu2[2,] = mu1[2,] + 1

Z1 = sample(5, n1, replace=TRUE)
Z2 = sample(5, n2, replace=TRUE)
X1 = mu1[Z1,] + matrix(rnorm(n1*p), ncol=p)
X2 = mu2[Z2,] + matrix(rnorm(n2*p), ncol=p)
X = rbind(X1, X2)
colnames(X) = c(1,2)
G = c(rep(1, n1), rep(2,n2))

ans = mrs(X, G, K=8)
plotTree(ans, type = "prob", legend = TRUE)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(MRS)
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/MRS/plotTree.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotTree
> ### Title: Plot nodes of the representative tree
> ### Aliases: plotTree
> 
> ### ** Examples
> 
> set.seed(1)
> p = 2
> n1 = 200
> n2 = 200
> mu1 = matrix( c(9,9,0,4,-2,-10,3,6,6,-10), nrow = 5, byrow=TRUE)
> mu2 = mu1; mu2[2,] = mu1[2,] + 1
> 
> Z1 = sample(5, n1, replace=TRUE)
> Z2 = sample(5, n2, replace=TRUE)
> X1 = mu1[Z1,] + matrix(rnorm(n1*p), ncol=p)
> X2 = mu2[Z2,] + matrix(rnorm(n2*p), ncol=p)
> X = rbind(X1, X2)
> colnames(X) = c(1,2)
> G = c(rep(1, n1), rep(2,n2))
> 
> ans = mrs(X, G, K=8)
> plotTree(ans, type = "prob", legend = TRUE)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>