compositions (version 1.40-2)

plot.aplus: Displaying amounts in scatterplots

Description

This function displays multivariate unclosed amout datasets classes "aplus" and "rplus" in a way respecting the choosen geometry eventually in log scale.

Usage

# S3 method for aplus
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"),
                     add=FALSE,logscale=TRUE,xlim=NULL,ylim=xlim,
                     col=par("col"),plotMissings=TRUE,
                     lenMissingTck=0.05,colMissingTck="red",
                     mp=~simpleMissingSubplot(missingPlotRect,missingInfo,
                                               c("NM","TM",cn)),
                     robust=getOption("robust"))
  # S3 method for rplus
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"),
                     add=FALSE,logscale=FALSE,
                     xlim=NULL,
                     ylim=xlim,col=par("col"),plotMissings=TRUE,
                     lenMissingTck=0.05,colMissingTck="red",
                     mp=~simpleMissingSubplot(missingPlotRect,missingInfo,
                                               c("NM","TM",cn)),
                     robust=getOption("robust"))
  # S3 method for rmult
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"),
                     add=FALSE,logscale=FALSE,col=par("col"),
                     robust=getOption("robust"))

Arguments

x

a dataset with class aplus, rplus or rmult

…

further graphical parameters passed (see par)

add

a logical indicating whether the information should just be added to an existing plot. If FALSE, a new plot is created

col

the color to plot the data

plotMissings

logical indicating that missingness should be represented graphically. Componentes with one missing subcomponent in the plot are represented by tickmarks at the two axis. Cases with two missing components are only represented in a special panel drawn according to the mp parameter if missings are present. Missings of type BDL (below detection limit) are always plotted in nonlogaritmic plots, even if plotMissings is false, but in this case this fact is not specially marked.

lenMissingTck

length of the tick-marks (in portion of the plotting region) to be plotted for missing values. If 0 no tickmarks are plotted. Negative lengths point outside of the plot. A length of 1 runs right through the whole plot.

colMissingTck

colors to draw the missing tick-marks. NULL means to take the colors specified for the observations.

mp

A formula providing a call to a function plotting informations on the missings. The call is evaluted in the environment of the panel plotting function and has access (among others) to: cn the names of the components in the current plot, x the dataset of the current plot, missingInfo is a table giving the number of observations of the types NM=Non Missing, TM=Totally missing (i.e. two components of the subcomposition are missing), and the two single component missing possibilities.

labels

the labels for 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 the data should be centered prior to the plot. Centering is done in the chosen geometry. See scale

scale

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

pca

a logical indicating whether the first principal component should be displayed in the plot. Currently, the direction of the principal component of the displayed subcomposition is displayed as a line. In a future, the projected principal componenent of the whole dataset should be displayed.

col.pca

the color to draw the principal component.

logscale

logical indicating whether a log scale should be used

xlim

2xncol(x)-matrix giving the xlims for the columns of x

ylim

2xncol(x)-matrix giving the ylims for the columns of x

robust

A robustness description. See robustnessInCompositions for details. The option is used for centering, scaling and principle components.

Details

TO DO: fix pca bug

See Also

plot.aplus, qqnorm.acomp,boxplot.acomp

Examples

# NOT RUN {
data(SimulatedAmounts)
plot(aplus(sa.lognormals))
plot(rplus(sa.lognormals))
plot(aplus(sa.lognormals5))
plot(rplus(sa.lognormals5))
# }