pairs {compositions}  R Documentation 
Pairs plot method for compositions
Description
Pairs plot function for compositions, allowing flexible representations.
Usage
## S3 method for class 'acomp'
pairs(x, labels, panel = vp.lrdensityplot, ...,
horInd = 1:ncol(x), verInd = 1:ncol(x),
lower.panel = panel, upper.panel = panel,
diag.panel = NULL, text.panel = textPanel,
label.pos = 0.5 + has.diag/3, line.main = 3,
cex.labels = NULL, font.labels = 1,
row1attop = TRUE, gap = 1, log = "")
## S3 method for class 'rcomp'
pairs(x, labels, panel = vp.diffdensityplot, ...,
horInd = 1:ncol(x), verInd = 1:ncol(x),
lower.panel = panel, upper.panel = panel,
diag.panel = NULL, text.panel = textPanel,
label.pos = 0.5 + has.diag/3, line.main = 3,
cex.labels = NULL, font.labels = 1,
row1attop = TRUE, gap = 1, log = "")
vp.lrdensityplot(x, y, col=2,..., alpha = NULL)
vp.diffdensityplot(x, y, col=2,..., alpha = NULL)
vp.lrboxplot(x, y, ...)
vp.kde2dplot(x, y, grid=TRUE, legpos="bottomright", colpalette=heat.colors,...)
Arguments
x 
a dataset of a compositional class; or for the panel functions, a vector of row components 
y 
for the panel functions, a vector of column components 
... 
further graphical parameters passed (see

labels 
the names of the parts 
panel 
common panel function to use for all offdiagonal plots 
horInd 
indices of columns of x to plot on the horizontal axis, defaults to all columns 
verInd 
indices of columns of x to plot on the vertical axis, defaults to all columns 
lower.panel 
panel function for the lower triangle of plots, defaults to the common panel 
upper.panel 
panel function for the uppper triangle of plots, defaults to the common panel 
diag.panel 
panel function for the diagonal of plots, defaults to text.panel 
text.panel 
panel function to write labels on the diagonal panels 
label.pos 
y position of labels in the text panel 
line.main 
if main is specified, line.main gives the line argument to mtext() which draws the title. You may want to specify oma when changing line.main 
cex.labels 
graphics parameters for the text panel 
font.labels 
graphics parameters for the text panel 
row1attop 
logical. Should the layout be matrixlike with row 1 at the top, or graphlike with row 1 at the bottom? 
gap 
distance between subplots, in margin lines 
log 
a character string indicating if logarithmic axes are to be used: see plot.default. Should not be used and left to the panel function to handle 
col 
color for density and histogram components of the panel vp.*density 
alpha 
alpha level for marking normality in the panels vp.*density; default to no mark 
grid 
should a unitgrid be added to each panel? 
legpos 
where should the legend be placed? to be given as 
colpalette 
which color palette is desired for the 2d density levels? 
Details
The data is displayed in a matrix of plots, after the indications of a panel function.
This is a simple implementation of pairs
compositional methods, the real
functionality is controlled by the panel functions.
The three panel functions included here can be used for generating either boxplots
or histograms plus kernel density plots of all pairwise logratios (in acomp) or
differences (in rcomp) of the components. In the cas of histograms, these
can be colored or left blackandwhite depending on the adjustment to
normality, controlled by a shapiro.test
and the alphalevel given.
These panel functions serve also as examples of how to generate user defined panels.
Author(s)
Raimon TolosanaDelgado
See Also
Examples
data(SimulatedAmounts)
pairs(acomp(sa.lognormals))
pairs(rcomp(sa.lognormals))