R: Displaying amounts in scatterplots

plot.aplus {compositions} | R Documentation

## 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 class '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 class '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 class '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

### Author(s)

K.Gerald v.d. Boogaart http://www.stat.boogaart.de

### See Also

`plot.aplus`, `qqnorm.acomp`,`boxplot.acomp`

### Examples

    data(SimulatedAmounts)
    plot(aplus(sa.lognormals))
    plot(rplus(sa.lognormals))
    plot(aplus(sa.lognormals5))
    plot(rplus(sa.lognormals5))

[Package compositions version 1.40-5 Index]