R: An S4 Lattice-Based Package for the Representation of Multivariate Data

# An S4 Lattice-Based Package for the Representation of Multivariate Data

## Documentation for package ‘adegraphics’ version 1.0-22

- DESCRIPTION file
- User guides, package vignettes and other documentation

## Help Pages

A B C G I K L N P R S T U Z misc

adegraphics-package | Graphical objects for ade4 functions (and more)

## -- A --

add.ADEg | Superpose an new 'ADEg' graph to the previous ones plotted
add.ADEg-method | Class 'ADEg'
add.ADEg-methods | Superpose an new 'ADEg' graph to the previous ones plotted
addhist | Adds histograms and density lines against a bi-dimensional graphics.
addhist-method | Adds histograms and density lines against a bi-dimensional graphics.
addhist-methods | Adds histograms and density lines against a bi-dimensional graphics.
addline | Adds lines on graphics.
addline-method | Adds lines on graphics.
addline-methods | Adds lines on graphics.
addpoint | Adds points on graphics.
addpoint-method | Adds points on graphics.
addpoint-methods | Adds points on graphics.
addsegment | Adds segments on graphics.
addsegment-method | Adds segments on graphics.
addsegment-methods | Adds segments on graphics.
addtext | Adds labels on graphics.
addtext-method | Adds labels on graphics.
addtext-methods | Adds labels on graphics.
ADEg | Class 'ADEg'
ADEg-class | Class 'ADEg'
ADEg.C1 | Class 'ADEg.C1'
ADEg.C1-class | Class 'ADEg.C1'
adeg.panel.edges | Panel functions for adding graphs.
adeg.panel.hist | Panel function for adding histograms.
adeg.panel.join | Panel function for joining lines.
adeg.panel.label | Panel function for adding labels.
adeg.panel.nb | Panel functions for adding graphs.
adeg.panel.Spatial | Panel function for adding spatial objects.
adeg.panel.values | Panel function drawing a third variable into a two-dimensional scatterplot
ADEg.S1 | Class 'ADEg.S1'
ADEg.S1-class | Class 'ADEg.S1'
ADEg.S2 | Class 'ADEg.S2'
ADEg.S2-class | Class 'ADEg.S2'
ADEg.T | Class 'ADEg.T'
ADEg.T-class | Class 'ADEg.T'
ADEg.Tr | Class '"ADEg.Tr"'
ADEg.Tr-class | Class '"ADEg.Tr"'
adegpar | Handling ADEg graphical parameters
adegraphics | Graphical objects for ade4 functions (and more)
ADEgS | Creation of 'ADEgS' objects
ADEgS-class | Class '"ADEgS"'

## -- B --

biplot | Methods to display the outputs of an analysis performed with 'ade4'
biplot.dudi | Methods to display the outputs of an analysis performed with 'ade4'

## -- C --

C1.barchart | Class 'C1.barchart'
C1.barchart-class | Class 'C1.barchart'
C1.curve | Class 'C1.curve'
C1.curve-class | Class 'C1.curve'
C1.curves | Class 'C1.curve'
C1.curves-class | Class 'C1.curve'
C1.density | Class 'C1.density'
C1.density-class | Class 'C1.density'
C1.dotplot | Class 'C1.dotplot'
C1.dotplot-class | Class 'C1.dotplot'
C1.gauss | Class 'C1.gauss'
C1.gauss-class | Class 'C1.gauss'
C1.hist | Class 'C1.hist'
C1.hist-class | Class 'C1.hist'
C1.interval | Class 'C1.interval'
C1.interval-class | Class 'C1.interval'
cbindADEg | Combine 'ADEg' objects by columns or rows
cbindADEg-method | Combine 'ADEg' objects by columns or rows
cbindADEg-methods | Combine 'ADEg' objects by columns or rows
changelatticetheme | Change the 'lattice' theme used for 'adegraphics'

## -- G --

getcall | Method for 'ADEg' and 'ADEgS' objects
getcall-method | Class 'ADEg'
getcall-method | Class '"ADEgS"'
getcall-methods | Method for 'ADEg' and 'ADEgS' objects
getgraphics | Class '"ADEgS"'
getgraphics-method | Class '"ADEgS"'
getlatticecall | Class 'ADEg'
getlatticecall-method | Class 'ADEg'
getparameters | Class 'ADEg'
getparameters-method | Class 'ADEg'
getpositions | Class '"ADEgS"'
getpositions-method | Class '"ADEgS"'
getstats | Class 'ADEg'
getstats-method | Class 'ADEg'
getstats-methods | Class 'ADEg'
gettrellis | Class 'ADEg'
gettrellis-method | Class 'ADEg'
gettrellis-method | Class 'ADEg.C1'
gettrellis-method | Class 'ADEg.S1'
gettrellis-method | Class 'ADEg.S2'
gettrellis-method | Class 'ADEg.T'
gettrellis-method | Class '"ADEg.Tr"'
gettrellis-methods | Class 'ADEg'

## -- I --

insert | Insert a graphic into an existing one
insert-method | Insert a graphic into an existing one
insert-methods | Insert a graphic into an existing one

## -- K --

kplot | Methods to display the outputs of an analysis performed with 'ade4'
kplot.foucart | Methods to display the outputs of an analysis performed with 'ade4'
kplot.mbpcaiv | Methods to display the outputs of an analysis performed with 'ade4'
kplot.mcoa | Methods to display the outputs of an analysis performed with 'ade4'
kplot.mfa | Methods to display the outputs of an analysis performed with 'ade4'
kplot.pta | Methods to display the outputs of an analysis performed with 'ade4'
kplot.sepan | Methods to display the outputs of an analysis performed with 'ade4'
kplot.statis | Methods to display the outputs of an analysis performed with 'ade4'
kplotsepan.coa | Methods to display the outputs of an analysis performed with 'ade4'

## -- L --

layout2position | Transform a layout matrix into a position one
length-method | Class '"ADEgS"'

## -- N --

names-method | Class '"ADEgS"'
names<--method | Class '"ADEgS"'

## -- P --

panel | Methods 'panel' for 'ADEg' objects
panel-method | Class 'C1.barchart'
panel-method | Class 'C1.curve'
panel-method | Class 'C1.density'
panel-method | Class 'C1.dotplot'
panel-method | Class 'C1.gauss'
panel-method | Class 'C1.hist'
panel-method | Class 'C1.interval'
panel-method | Class 'S1.boxplot'
panel-method | Class 'S1.class'
panel-method | Class 'S1.distri'
panel-method | Class 'S1.label'
panel-method | Class 'S1.match'
panel-method | Class 'S2.arrow'
panel-method | Class 'S2.class'
panel-method | Class 'S2.corcircle'
panel-method | Class 'S2.density'
panel-method | Class 'S2.distri'
panel-method | Class 'S2.image'
panel-method | Class 'S2.label'
panel-method | Class 'S2.logo'
panel-method | Class 'S2.match'
panel-method | Class 'S2.traject'
panel-method | Class 'S2.value'
panel-method | Class 'T.cont'
panel-method | Class 'T.image'
panel-method | Class 'T.value'
panel-method | Class 'Tr.class'
panel-method | Class 'Tr.label'
panel-method | Class 'Tr.match'
panel-method | Class 'Tr.traject'
panel-methods | Methods 'panel' for 'ADEg' objects
panelbase | Class 'ADEg'
panelbase-method | Class 'ADEg'
panelbase-method | Class 'ADEg.C1'
panelbase-method | Class 'ADEg.S1'
panelbase-method | Class 'ADEg.S2'
panelbase-method | Class 'ADEg.T'
panelbase-method | Class '"ADEg.Tr"'
panelbase-methods | Class 'ADEg'
plot | Methods to display the outputs of an analysis performed with 'ade4'
plot-method | Class 'ADEg'
plot-method | Class '"ADEgS"'
plot.acm | Methods to display the outputs of an analysis performed with 'ade4'
plot.bcaloocv | Methods to display the outputs of an analysis performed with 'ade4'
plot.betcoi | Methods to display the outputs of an analysis performed with 'ade4'
plot.betdpcoa | Methods to display the outputs of an analysis performed with 'ade4'
plot.betrlq | Methods to display the outputs of an analysis performed with 'ade4'
plot.between | Methods to display the outputs of an analysis performed with 'ade4'
plot.betwitdpcoa | Methods to display the outputs of an analysis performed with 'ade4'
plot.coinertia | Methods to display the outputs of an analysis performed with 'ade4'
plot.discloocv | Methods to display the outputs of an analysis performed with 'ade4'
plot.discrimin | Methods to display the outputs of an analysis performed with 'ade4'
plot.dpcoa | Methods to display the outputs of an analysis performed with 'ade4'
plot.fca | Methods to display the outputs of an analysis performed with 'ade4'
plot.foucart | Methods to display the outputs of an analysis performed with 'ade4'
plot.inertia | Display the decomposition of inertia which measure the contributions of rows/columns in mutivariate methods
plot.krandboot | Methods to display the outputs of an analysis performed with 'ade4'
plot.krandxval | Methods to display the outputs of an analysis performed with 'ade4'
plot.mcoa | Methods to display the outputs of an analysis performed with 'ade4'
plot.mfa | Methods to display the outputs of an analysis performed with 'ade4'
plot.multiblock | Methods to display the outputs of an analysis performed with 'ade4'
plot.multispati | Methods to display the outputs of an analysis performed with 'ade4'
plot.niche | Methods to display the outputs of an analysis performed with 'ade4'
plot.pcaiv | Methods to display the outputs of an analysis performed with 'ade4'
plot.procuste | Methods to display the outputs of an analysis performed with 'ade4'
plot.pta | Methods to display the outputs of an analysis performed with 'ade4'
plot.randboot | Methods to display the outputs of an analysis performed with 'ade4'
plot.randxval | Methods to display the outputs of an analysis performed with 'ade4'
plot.rlq | Methods to display the outputs of an analysis performed with 'ade4'
plot.sepan | Methods to display the outputs of an analysis performed with 'ade4'
plot.statis | Methods to display the outputs of an analysis performed with 'ade4'
plot.witcoi | Methods to display the outputs of an analysis performed with 'ade4'
plot.witdpcoa | Methods to display the outputs of an analysis performed with 'ade4'
plot.within | Methods to display the outputs of an analysis performed with 'ade4'
plot.witrlq | Methods to display the outputs of an analysis performed with 'ade4'
plotEig | Plot a barchart of eigen values
prepare | Methods 'prepare' for 'ADEg' objects
prepare-method | Class 'ADEg.C1'
prepare-method | Class 'ADEg.S1'
prepare-method | Class 'ADEg.S2'
prepare-method | Class 'ADEg.T'
prepare-method | Class '"ADEg.Tr"'
prepare-method | Class 'C1.barchart'
prepare-method | Class 'C1.curve'
prepare-method | Class 'C1.density'
prepare-method | Class 'C1.dotplot'
prepare-method | Class 'C1.gauss'
prepare-method | Class 'C1.hist'
prepare-method | Class 'C1.interval'
prepare-method | Class 'S1.boxplot'
prepare-method | Class 'S1.class'
prepare-method | Class 'S1.distri'
prepare-method | Class 'S1.label'
prepare-method | Class 'S1.match'
prepare-method | Class 'S2.arrow'
prepare-method | Class 'S2.class'
prepare-method | Class 'S2.corcircle'
prepare-method | Class 'S2.density'
prepare-method | Class 'S2.distri'
prepare-method | Class 'S2.image'
prepare-method | Class 'S2.label'
prepare-method | Class 'S2.logo'
prepare-method | Class 'S2.match'
prepare-method | Class 'S2.traject'
prepare-method | Class 'S2.value'
prepare-method | Class 'T.image'
prepare-method | Class 'T.value'
prepare-method | Class 'Tr.class'
prepare-method | Class 'Tr.label'
prepare-method | Class 'Tr.match'
prepare-method | Class 'Tr.traject'
prepare-methods | Methods 'prepare' for 'ADEg' objects
print-method | Class 'ADEg'
print-method | Class '"ADEgS"'
printSuperpose-method | Class 'ADEg'

## -- R --

rbindADEg | Combine 'ADEg' objects by columns or rows
rbindADEg-method | Combine 'ADEg' objects by columns or rows
rbindADEg-methods | Combine 'ADEg' objects by columns or rows

## -- S --

s.arrow | 2-D scatter plot with arrows
s.class | 2-D scatter plot with a partition in classes (levels of a factor)
s.corcircle | Correlation circle
s.density | 2-D scatter plot with kernel density estimation
s.distri | 2-D scatter plot with means/standard deviations computed using an external table of weights
s.image | 2-D scatter plot with loess estimation of an additional numeric score (levelplot)
s.label | 2-D scatter plot with labels
s.logo | 2-D scatter plot with logos (bitmap objects)
s.match | 2-D scatter plot of the matching between two sets of coordinates
s.Spatial | Mapping of a Spatial* object
s.traject | 2-D scatter plot with trajectories
s.value | 2-D scatter plot with proportional symbols (bubble plot)
S1.boxplot | Class 'S1.boxplot'
S1.boxplot-class | Class 'S1.boxplot'
S1.class | Class 'S1.class'
S1.class-class | Class 'S1.class'
S1.distri | Class 'S1.distri'
S1.distri-class | Class 'S1.distri'
S1.label | Class 'S1.label'
S1.label-class | Class 'S1.label'
S1.match | Class 'S1.match'
S1.match-class | Class 'S1.match'
s1d.barchart | 1-D plot of a numeric score by bars
s1d.boxplot | 1-D box plot of a numeric score partitioned in classes (levels of a factor)
s1d.class | 1-D plot of a numeric score partitioned in classes (levels of a factor)
s1d.curve | 1-D plot of a numeric score linked by curves
s1d.curves | 1-D plot of multiple scores linked by curves
s1d.density | 1-D plot of a numeric score by density curves
s1d.distri | 1-D plot of a numeric score by means/standard deviations computed using an external table of weights
s1d.dotplot | 1-D plot of a numeric score by dots
s1d.gauss | 1-D plot of a numeric score by Gaussian curves
s1d.hist | 1-D plot of a numeric score by bars
s1d.interval | 1-D plot of the interval between two numeric scores
s1d.label | 1-D plot of a numeric score with labels
s1d.match | 1-D plot of the matching between two numeric scores
S2.arrow | Class 'S2.arrow'
S2.arrow-class | Class 'S2.arrow'
S2.class | Class 'S2.class'
S2.class-class | Class 'S2.class'
S2.corcircle | Class 'S2.corcircle'
S2.corcircle-class | Class 'S2.corcircle'
S2.density | Class 'S2.density'
S2.density-class | Class 'S2.density'
S2.distri | Class 'S2.distri'
S2.distri-class | Class 'S2.distri'
S2.image | Class 'S2.image'
S2.image-class | Class 'S2.image'
S2.label | Class 'S2.label'
S2.label-class | Class 'S2.label'
S2.logo | Class 'S2.logo'
S2.logo-class | Class 'S2.logo'
S2.match | Class 'S2.match'
S2.match-class | Class 'S2.match'
S2.traject | Class 'S2.traject'
S2.traject-class | Class 'S2.traject'
S2.value | Class 'S2.value'
S2.value-class | Class 'S2.value'
scatter | Methods to display the outputs of an analysis performed with 'ade4'
scatter.coa | Methods to display the outputs of an analysis performed with 'ade4'
scatter.dudi | Methods to display the outputs of an analysis performed with 'ade4'
scatter.nipals | Methods to display the outputs of an analysis performed with 'ade4'
scatter.pco | Methods to display the outputs of an analysis performed with 'ade4'
score | Methods to display the outputs of an analysis performed with 'ade4'
score.acm | Methods to display the outputs of an analysis performed with 'ade4'
score.inertia | Display the decomposition of inertia which measure the contributions of rows/columns in mutivariate methods
score.mix | Methods to display the outputs of an analysis performed with 'ade4'
score.pca | Methods to display the outputs of an analysis performed with 'ade4'
screeplot | Methods to display the outputs of an analysis performed with 'ade4'
screeplot.dudi | Methods to display the outputs of an analysis performed with 'ade4'
setlatticecall-method | Class 'ADEg.C1'
setlatticecall-method | Class 'ADEg.S1'
setlatticecall-method | Class 'ADEg.S2'
setlatticecall-method | Class 'ADEg.T'
setlatticecall-method | Class '"ADEg.Tr"'
setlatticecall-method | Class 'S1.boxplot'
setlimits1D | Computes limits for 1D and 2D displays.
setlimits2D | Computes limits for 1D and 2D displays.
show-method | Class 'ADEg'
show-method | Class '"ADEgS"'
sortparamADEg | Sort a sequence of graphical parameters
sortparamADEgS | Sort a sequence of graphical parameters
superpose | Superpose two graphics
superpose-method | Superpose two graphics
superpose-methods | Superpose two graphics

## -- T --

T.cont | Class 'T.cont'
T.cont-class | Class 'T.cont'
T.image | Class 'T.image'
T.image-class | Class 'T.image'
T.value | Class 'T.value'
T.value-class | Class 'T.value'
table.image | Heat map-like representation with colored cells
table.value | Heat map-like representation with proportional symbols
Tr.class | Class 'Tr.class'
Tr.class-class | Class 'Tr.class'
Tr.label | Class 'Tr.label'
Tr.label-class | Class 'Tr.label'
Tr.match | Class 'Tr.match'
Tr.match-class | Class 'Tr.match'
Tr.traject | Class 'Tr.traject'
Tr.traject-class | Class 'Tr.traject'
triangle.class | Ternary plot with a partition in classes (levels of a factor)
triangle.label | Ternary plot with labels
triangle.match | Ternary plot of the matching between two sets of coordinates
triangle.traject | Ternary plot with trajectories

## -- U --

update,ADEg | Class 'ADEg'
update,ADEgS | Class '"ADEgS"'
update-method | Class 'ADEg'
update-method | Class '"ADEgS"'

## -- Z --

zoom | Zoom in or out
zoom-method | Zoom in or out
zoom-methods | Zoom in or out

## -- misc --

$-method | Class '"ADEgS"'
+-method | Superpose two graphics
+-methods | Superpose two graphics
[-method | Class '"ADEgS"'
[[-method | Class '"ADEgS"'
[[<--method | Class '"ADEgS"'
\S4method{+}{ADEg} | Superpose two graphics