panel.elli: Panel Function for Plotting Ellipse and outlier

In mt: Metabolomics Data Analysis Toolbox

Description

lattice panel functions for plotting grouped ellipse and outlier

Usage

panel.elli(x, y, groups = NULL,conf.level = 0.975, ...)
panel.elli.1(x, y, subscripts, groups=NULL, conf.level = 0.975,
             ep=0, com.grp=NULL, no.grp=NULL, ell.grp=NULL, ...)
panel.outl(x, y, subscripts, groups=NULL, conf.level = 0.975, labs, ...)

Arguments

x, y	Variables to be plotted.
conf.level	Confident level for ellipse
groups, subscripts	Internal parameters for Lattice.
labs	Labels for potential outliers.
ep	An integer for plotting ellipse. 1 and 2 for plotting overall and group ellipse, respectively. Otherwise, none.
com.grp	A list of characters to select which combination of groups to be plotted.
no.grp	A list of characters to select which individual group not to be plotted. Note it will be overridden by com.grp. If no com.grp and no.grp, ellipses of each individual group will be plotted.
ell.grp	Another categorical vector used for plotting ellipse. If provided, ep,com.grp and no.grp will be ignored. It should be different from default groups, but has the same length of groups. For details, see example below.
...	Further arguments. See corresponding entry in xyplot for non-trivial details.

Details

panel.elli is modified from function panel.ellipse in package latticeExtra.

panel.elli.1 gives more control on how to plot ellipse for the current group. It also provides an option to plot ellipse based on another user-defined groups.

panel.outl plots the labels of data points outside the ellipse. These data points can be treated as potential outliers.

Value

Retuns objects of class "trellis".

Note

panel.elli.1 can be called by functions grpplot, pcaplot, mdsplot, pca.plot.wrap, mds.plot.wrap, pls.plot.wrap and lda.plot.wrap by passing argument of ep. See examples of these function for details.

Author(s)

Wanchang Lin

See Also

grpplot, pcaplot, mdsplot.

Examples

library(lattice) 
data(iris)

## =====================================================================
## Examples of calling 'panel.elli' and 'panel.outl'
xyplot(Sepal.Length ~ Petal.Length, data = iris, groups=Species,
        par.settings = list(superpose.symbol = list(pch=c(15:17)),
                            superpose.line = list(lwd=2, lty=1:3)),
        panel = function(x, y, ...) {
            panel.xyplot(x, y, ...)
            panel.elli(x, y, ..., type="l",lwd=2)
            panel.outl(x,y, ...)
        },
        auto.key = list(x = .1, y = .8, corner = c(0, 0)),
        labs=rownames(iris), conf.level=0.9,adj = -0.5)

## Without groups
xyplot(Sepal.Length ~ Petal.Length, data = iris,
        par.settings = list(plot.symbol = list(cex = 1.1, pch=16)),
        panel = function(x, y, ...) {
            panel.xyplot(x, y, ...)
            panel.elli(x, y, ..., type="l", lwd = 2)
            panel.outl(x,y, ...)
        },
        auto.key = list(x = .1, y = .8, corner = c(0, 0)),
        labs=rownames(iris), conf.level=0.9,adj = -0.5)


## With conditioning
xyplot(Sepal.Length ~ Petal.Length|Species, data = iris, 
        par.settings = list(plot.symbol = list(cex = 1.1, pch=16)),
        layout=c(2,2),
        panel = function(x, y, ...) {
            panel.xyplot(x, y, ...)
            panel.elli(x, y, ..., type="l", lwd = 2)
            panel.outl(x,y, ...)
        },
        auto.key = list(x = .6, y = .8, corner = c(0, 0)),
        adj = 0,labs=rownames(iris), conf.level=0.95)

## =====================================================================
## Examples of 'panel.elli.1'
xyplot(Sepal.Length ~ Petal.Length, data = iris, groups=Species,
        ## ---------------------------------------------------
        ## Select what to be plotted.
        ep=2,
        ## com.grp = list(a="setosa",b=c("versicolor", "virginica")),
        ## no.grp = "setosa", ## Not draw ellipse for "setosa"
        ## ---------------------------------------------------
        par.settings = list(superpose.symbol = list(pch=c(15:17)),
                            superpose.line = list(lwd=2, lty=1:3)),
        panel = function(x, y, ...) {
            panel.xyplot(x, y, ...)
            panel.elli.1(x, y, ...)
            panel.outl(x,y, ...)
        },
        auto.key = list(points = TRUE, rectangles = FALSE, space = "right"),
        adj = 0,labs=rownames(iris), conf.level=0.95)

xyplot(Sepal.Length ~ Petal.Length, data = iris, groups=Species,
        ## ---------------------------------------------------
        ## Select what to be plotted.
        ep=2,
        ## com.grp = list(a="setosa",b=c("versicolor", "virginica")),
        no.grp = c("setosa","versicolor"),## Only draw "virginica"
        ## ---------------------------------------------------
        par.settings = list(superpose.symbol = list(pch=c(15:17)),
                            superpose.line = list(lwd=2, lty=1:3)),
        panel = function(x, y, ...) {
            panel.xyplot(x, y, ...)
            panel.elli.1(x, y, ...)
        },
        auto.key = list(x = .1, y = .8, corner = c(0, 0)))

xyplot(Sepal.Length ~ Petal.Length, data = iris, groups=Species,
        ## ---------------------------------------------------
        ## Select what to be plotted.
        ep=2,
        com.grp = list(a="setosa",b=c("versicolor", "virginica")),
        ## no.grp = "setosa", ## Not draw ellipse for "setosa"
        ## ---------------------------------------------------
        par.settings = list(superpose.symbol = list(pch=c(15:17)),
                            superpose.line = list(lwd=2, lty=1:3)),
        panel = function(x, y, ...) {
            panel.xyplot(x, y, ...)
            panel.elli.1(x, y, ...)
        },
        auto.key = list(x = .1, y = .8, corner = c(0, 0)))

  xyplot(Sepal.Length ~ Petal.Length, data = iris, groups=Species, ep=1,
        par.settings = list(superpose.symbol = list(pch=c(15:17)),
                            superpose.line = list(lwd=2, lty=1:3)),
        panel = function(x, y, ...) {
            panel.xyplot(x, y, ...)
            panel.elli.1(x, y, ...)
        },
        auto.key = list(points = TRUE, rectangles = FALSE, space = "right"))

## =====================================================================
## Another data set from package MASS
require(MASS)
data(Cars93)

## Plot ellipse based on original groups: DriveTrain
xyplot(Price~EngineSize, data=Cars93, groups=DriveTrain, ep=2,
        par.settings = list(superpose.symbol = list(pch=c(15:17)),
                            superpose.line = list(lwd=2, lty=1:3)),
        panel = function(x, y, ...) {
            panel.xyplot(x, y, ...)
            panel.elli.1(x, y, ...)
        },
        auto.key = list(points = TRUE, rectangles = FALSE, space = "right"))

## But we want to plot ellipse using AirBags
xyplot(Price~EngineSize, data=Cars93, groups=DriveTrain, 
        ell.grp=Cars93$AirBags,
        par.settings = list(superpose.symbol = list(pch=c(15:17)),
                            superpose.line = list(lwd=2, lty=1:3)),
        panel = function(x, y, ...) {
            panel.xyplot(x, y, ...)
            panel.elli.1(x, y, ...)
        },
        auto.key = list(points = TRUE, rectangles = FALSE, space = "right"))

mt documentation built on Feb. 2, 2022, 1:07 a.m.