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Last data update: 2014.03.03

R: Pairwise Scatterplot Matrix of Shape Matrices

plotShape

R Documentation

Pairwise Scatterplot Matrix of Shape Matrices

Description

Function for visual comparisons for up to three shape matrices.

Usage

plotShape(est1, est2 = NULL, est3 = NULL, X = NULL, alim = NULL, 
          color.ell = 2:4, color.points = grey(0.5), 
          lty.ell = rep(1, 3), pch.ell = rep(16, 3), 
          lwd.ell = rep(1, 3), cex.ell = rep(1, 3),  
          pch.points = 1, level = 0.5, npoints = 100, 
          x.legend, y.legend, cex.legend = 1, pty = "s", gap = 1, 
          oma.bottom, labels, cex.labels = 2, main, ...)

Arguments

`est1`	The shape matrix of interest. A list with the components `location`, `scatter` and `est.name`.
`est2`	An optional additional shape matrix. A list with the components `location`, `scatter` and `est.name`.
`est3`	An optional additional shape matrix. A list with the components `location`, `scatter` and `est.name`.
`X`	a numeric data frame or matrix. Optional data points on which the estimates could have been based.
`alim`	can be `NULL`, `both` or `ellipses`. Specifies when the plotting regions are computed if only the size of the ellipses are to be considered or also the range of the data points. If `NULL` it chooses `both` if `X` is provided and otherwise `ellipses`.
`color.ell`	vector of length 3 that gives the colors for the corresponding estimates `'est1'`, `'est2'` and `'est3'`.
`color.points`	the color of the data points.
`lty.ell`	line types of the confidence ellipsoids.
`pch.ell`	plotting symbols for the location estimates, the centers of the confidence ellipsoids.
`lwd.ell`	line width values of the confidence ellipsoids.
`cex.ell`	cex values for the location estimates, the centers of the confidence ellipsoids.
`pch.points`	plotting symbol for the data points `X`.
`level`	The proportion of the data points that should be inside the ellipses. If there is no data the value for `t` in the function `ellipse`.
`npoints`	the number of points used to approximate each ellipsoid.
`x.legend`	vertical position of the legend. By default tries to find for 2 to 4 dimensional data a good location. If `NULL` no legend is drawn.
`y.legend`	horicontal position of the legend. By default tries to find for 2 to 4 dimensional data a good location. If `NULL` no legend is drawn.
`cex.legend`	`cex` for the legend.
`pty`	`pty` value for the individual plots of the scatter matrix. Default is `"s"`.
`gap`	distance between subplots, in margin lines.
`oma.bottom`	`oma` value of the bottom.
`labels`	optional labels for the diagonals.
`cex.labels`	`cex` for the labels. Default is 2.
`main`	optional title of the plot.
`...`	further arguments passed to or from other methods.

Details

All scatter matrices are standardized to have determinant 1. If X is given, the Mahalanobis distances based on the location and shape estimates are computed, and t in the function ellipse is the level quantile of the Mahalanobis distances. If no X is provided t equals level.

The location of the legend is currently problematic and it is recommended that the user should provide the coordinates for the legend.

Value

A scatter plot matrix.

Author(s)

Klaus Nordhausen

Examples

X <- rmvt(100, diag(3), df=3)

EST1 <- list(location=colMeans(X), scatter=cov(X), est.name="COV")
HR <- HR.Mest(X)
EST2 <- list(location=HR$center, scatter=HR$scatter, est.name="Tyler")
plotShape(EST1,EST2, X=X)

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(MNM)
Loading required package: ICSNP
Loading required package: mvtnorm
Loading required package: ICS
Loading required package: SpatialNP
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/MNM/plotShape.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotShape
> ### Title: Pairwise Scatterplot Matrix of Shape Matrices
> ### Aliases: plotShape
> ### Keywords: hplot
> 
> ### ** Examples
> 
> X <- rmvt(100, diag(3), df=3)
> 
> EST1 <- list(location=colMeans(X), scatter=cov(X), est.name="COV")
> HR <- HR.Mest(X)
> EST2 <- list(location=HR$center, scatter=HR$scatter, est.name="Tyler")
> plotShape(EST1,EST2, X=X)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>