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Last data update: 2014.03.03

R: Plot regions of the representative tree in 2D

plot2D

R Documentation

Plot regions of the representative tree in 2D

Description

This function visualizes the regions of the representative tree of the output of the mrs function.

Usage

plot2D(ans, type = "prob", data.points = "all", background = "none",
  group = 1, dim = c(1, 2),
  levels = sort(unique(ans$RepresentativeTree$Levels)), regions = rep(1,
  length(ans$RepresentativeTree$Levels)), legend = FALSE, main = "default")

Arguments

`ans`	An `mrs` object.
`type`	Different options on how to visualize the rectangular regions. The options are `type = c("eff", "prob", "empty", "none")`. Default is `type = "prob"`.
`data.points`	Different options on how to plot the data points. The options are `data.points = c("all", "differential", "none")`. Default is `data.points = "all"`.
`background`	Different options on the background. The options are `background = c("smeared", "none")` .
`group`	If `type = "eff"`, which group effect size is used. Default is `group = 1`.
`dim`	If the data are multivariate, `dim` are the two dimensions plotted. Default is `dim = c(1,2)`.
`levels`	Vector with the level of the regions to plot. The default is to plot regions at all levels.
`regions`	Binary vector indicating the regions to plot. The default is to plot all regions.
`legend`	Color legend for type. Default is `legend = FALSE`.
`main`	Overall title for the legend.

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)
plot2D(ans, type = "prob", legend = TRUE)

plot2D(ans, type="empty", data.points = "differential",
 background = "none")

plot2D(ans, type="none", data.points = "differential",
 background = "smeared", levels = 4)

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/plot2D.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plot2D
> ### Title: Plot regions of the representative tree in 2D
> ### Aliases: plot2D
> 
> ### ** 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)
> plot2D(ans, type = "prob", legend = TRUE)
> 
> plot2D(ans, type="empty", data.points = "differential",
+  background = "none")
> 
> plot2D(ans, type="none", data.points = "differential",
+  background = "smeared", levels = 4)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>