compositions (version 0.9-11)

plot.acomp: Displaying compositions in ternary diagrams

Usage

## S3 method for class 'acomp':
plot(x,...,labels=colnames(X),cn=colnames(X),aspanel=FALSE,id=FALSE,idlabs=NULL,idcol=2,center=FALSE,scale=FALSE,pca=FALSE,col.pca=par("col"),margin="acomp",add=FALSE,triangle=!add,col=par("col"))
## S3 method for class 'rcomp':
plot(x,...,labels=colnames(X),cn=colnames(X),aspanel=FALSE,id=FALSE,idlabs=NULL,idcol=2,center=FALSE,scale=FALSE,pca=FALSE,col.pca=par("col"),margin="rcomp",add=FALSE,col=par("col"))

Arguments

x

a dataset of a compositional class

...

further graphical parameters passed (see par)

margin

The type of marginalisation to be computed, when displaying the individual panels. Possible values are: "acomp", "rcomp" and any of the variable names/column numbers in the composition. If one of the columns is select

add

a logical indicating whether the information should just be added to an existing plot. In case of false a new plot is created.

triangle

A logical indicating whether the triangle should be drawn.

col

The color to plot the data.

labels

The names of the parts

cn

The names of the parts to be used in a single panel. Internal use only.

aspanel

Logical indicating that only a single panel should be drawn and not the whole plot. Internal use only.

id

A logical. If true one can identify the points like with the identify command.

idlabs

A character vector providing the labels to be used with the identification, when id=TRUE

idcol

color of the idlabs-labels

center

a logical indicating whether a the data should be centered prior to the plot. Centering is done in the choosen philosophy. See scale

scale

a logical indicating whether a the data should be scaled prior to the plot. Scaling is done in the choosen philosophy. See scale

pca

A logical indicating whether the first principle component should be displayed in the plot. Currently direction of the principle component of the displayed subcomposition is displayed as a line. Later on a the principle componenent of the

col.pca

The color to draw the principle component.

Details

The data is displayed in ternary diagrams. This does not work for two part compositions. Compositions of three parts are displayed in a single ternary diagram. For compositions of more than three components, the data is arrange in a scatterplot matrix through the command pairs. The third component in each of the panels is than choosen according to setting of margin=. Possible values of margin= are: "acomp", "rcomp" and any of the variable names/column numbers in the composition. If one of the columns is selected each panel displays a subcomposition given by the row part, the column part and the given part. If one of the classes is given the corresponding margin acompmargin or rcompmargin is used. Ternary diagrams can be read in multiple ways. Each corner of the triangle corresponds to a composition only containing the single part displayed in that corner. Points on the edges correspond to compositions only containing the parts in the adjacent corners. The relative amounts are displayed by the distance to the opposite corner. The individual portions of general points can be infered by imaginatorily drawing a line parallel to the edge opposite to the corner of the part of interest through the point. The portion of the part of intrest is constant along the line. Thus we can read it on both crossing points of the line with the edges. Relative portions of two parts can be inferred by imaginatorily drawing a line through the point and the corner of the unimportant component. This line intersects the edge between the two components of interest in the composition with the same relative portion of the two remaining components. Exactly the lines parallel to one of the edges or going through one of the corners are straight lines as well in Aitchison and as in real geometry. They remain straight under an arbitrary perturbation.

References

Aitchison, J. (1986) The Statistical Analysis of Compositional Data Monographs on Statistics and Applied Probability. Chapman & Hall Ltd., London (UK). 416p. Aitchison, J, C. Barcel'o-Vidal, J.J. Egozcue, V. Pawlowsky-Glahn (2002) A consise guide to the algebraic geometric structure of the simplex, the sample space for compositional data analysis, Terra Nostra, Schriften der Alfred Wegener-Stiftung, 03/2003 Billheimer, D., P. Guttorp, W.F. and Fagan (2001) Statistical interpretation of species composition, Journal of the American Statistical Association, 96 (456), 1205-1214 Pawlowsky-Glahn, V. and J.J. Egozcue (2001) Geometric approach to statistical analysis on the simplex. SERRA 15(5), 384-398 http://ima.udg.es/Activitats/CoDaWork03 http://ima.udg.es/Activitats/CoDaWork05

See Also

plot.aplus, kingTetrahedron (for 3D-plot), qqnorm.acomp,boxplot.acomp

Examples

data(SimulatedAmounts)
plot(acomp(sa.lognormals))
plot(rcomp(sa.lognormals))
plot(acomp(sa.lognormals5),pca=TRUE)
plot(rcomp(sa.lognormals5),pca=TRUE)