Package 'adegraphics'

Description

This package was created to replace graphics functionalities of the ade4 package and to offer customizable representations of data and result analysis.

Graphics are objects of S4 class, which can be displayed but also stored for latter modifications. Those modifications can be graphical changes, but also superposition or juxtaposition of various graphical objects (creating an other type of object). Each object will contain graphical parameters and instructions for the display (calls, positions, etc.) and the data set used. Sometimes data is heavy, due to its size for example. Two storing systems exist:

• full storage: data is assigned to an object's slot.

• names and position: data names (as a string, obtained using deparse(substitute)) and their frame position (using sys.nframe()) are stored. Then the full data can be retrieve with those two informations (and only if the data objects are still in the environment)

This new system is based on the lattice package and grid graphics.

Details

A lot of classes were implemented. Two superclass structures the architecture in class. Simple and complex graphics are distinguished in the former version:

• ADEg class provides simple graphics using one kind of data (most of a time, only a data frame) and one representation method (points, labels, arrows...)

• ADEgS class provides complex graphics making juxtaposition, superposition and/or insertion of several simple graphics.

5 subclasses inherits from the superclass abstract ADEg:

• ADEg.S1: one-dimensional plot

• ADEg.S2: bi-dimensional plot

• ADEg.C1: one-dimensional data plotted in 2-D

• ADEg.T: table plot

• ADEg.Tr: triangle plot

References

Aurélie Siberchicot, Alice Julien-Laferrière, Anne-Béatrice Dufour, Jean Thioulouse and Stéphane Dray (2017). adegraphics: An S4 Lattice-Based Package for the Representation of Multivariate Data. The R Journal. 9:2. 198–212. https://journal.r-project.org/archive/2017/RJ-2017-042/index.html

See Also

lattice ADEg ADEgS

Examples

showClass("ADEg")
  showClass("ADEgS")

Description

Adds an ADEg to the current ADEg or ADEgS plot.

Usage

add.ADEg(object)

Arguments

Details

This function uses the last plotted ADEg or ADEgS object.
It calls superpose.

Value

an ADEgS object

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot [email protected] and Stephane Dray

See Also

superpose ADEg ADEgS

Examples

df1 <- cbind(rnorm(24), rnorm(24))
df2 <- cbind(rnorm(24), rnorm(24))
g1 <- s.label(df1, ppoints.col = "blue")
g2 <- s.label(df2, ppoints.col = "red", plot = FALSE)
add.ADEg(g2)

data(jv73, package = "ade4")
pca1 <- ade4::dudi.pca(jv73$morpho, scannf = FALSE)
g5 <- s.label(pca1$li, plabels.optim = TRUE)
g6 <- s.class(pca1$li, jv73$fac.riv, starSize = 0, ellipseSize = 0, chullSize = 1, 
  ppolygons.alpha = 0.4, col = rainbow(12), ppoints.cex = 0, plot = FALSE)
add.ADEg(g6)

Description

Adds the two marginal histograms and density lines of each axis against an ADEg.S2 object.

Usage

addhist(object, bandwidth, gridsize = 60, kernel = "normal", cbreaks = 2, 
  storeData = TRUE, plot = TRUE, pos = -1, ...)

Arguments

Details

Density is calculated using the function bkde of the KernSmooth package.

Value

An ADEgS object, a list of four graphical objects, one ADEg.S2 and three trellis (from lattice). Their names are:

Note

Into the dots arguments, the usual parameters for the s.label can be given with the object key.

Trellis parameters are used for the three remaining graphics. plot.polygon handles the histogram aspect, add.line the graduations lines and plot.line the density lines.

Finally, for the link graphic, labels aspect can be changed using a plabels list, as for an S2.label object.

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot [email protected] and Stephane Dray

See Also

ADEg.S2 ADEgS

Examples

data(rpjdl, package = "ade4")
coa1 <- ade4::dudi.coa(rpjdl$fau, scannf = FALSE, nf = 4)
labli <- s.label(coa1$li)
g1 <- addhist(labli)
g2 <- addhist(labli, plabels.cex = 0, cbreaks = 3)
labco <- s.label(coa1$co)
g3 <- addhist(labco, plabels.cex = 0, cbreaks = 3)
update(g3, pbackground.col = "grey85")

Description

Adds a trellis object containing one or several lines on one or several graphical objects.

Usage

addline(object, a = NULL, b = 0, h = NULL, v = NULL, plot = TRUE, ...)

Arguments

Value

An object of class ADEgS.

Author(s)

Aurelie Siberchicot [email protected] and Stephane Dray

See Also

ADEg ADEgS panel.abline

Examples

# example extracted from the pedagogic file, here: http://pbil.univ-lyon1.fr/R/pdf/tdr65.pdf
data(monde84, package = "ade4")
dfX <- cbind.data.frame(lpib = log(monde84$pib), croipop = monde84$croipop)
dfY <- cbind.data.frame(lmorta = log(monde84$morta), lanal = log(monde84$anal + 1), 
  rscol = sqrt(100 - monde84$scol))
dfX0 <- ade4::scalewt(dfX)
dfY0 <- ade4::scalewt(dfY)
can1 <- cancor(dfX0, dfY0)
varcanoX <- dfX0 %*% can1$xcoef[,1]
varcanoY <- dfY0 %*% can1$ycoef[,1]
g1 <- s.label(cbind(varcanoY,varcanoX), labels = row.names(monde84), plabel.cex = 0.8, plot = FALSE)
addline(g1, 0, 1, plines.col = "red", plines.lwd = 0.5, plines.lty = 2)

Description

Adds a trellis object containing one or several points on one or several graphical objects.

Usage

addpoint(object, xcoord, ycoord, plot = TRUE, ...)

Arguments

Value

An object of class "ADEgS".

Author(s)

Aurelie Siberchicot [email protected] and Stephane Dray

See Also

ADEg ADEgS panel.points

Examples

data(deug, package = "ade4")
deug$cent[1]
g1 <- s1d.density(deug$tab[, 1], plot = FALSE)
addpoint(g1, xcoord = deug$cent[1], ycoord = 0, ppoints = list(col = "black",
  pch = "*", cex = 3))

Description

Adds a trellis object containing one or several segments on one or several graphical objects.

Usage

addsegment(object, x0 = NULL, y0 = NULL, x1, y1, plot = TRUE, ...)

Arguments

Details

x0, y0, x1 and y1 can be vectors. A line segment is drawn, for each i, between the point (x0[i], y0[i]) and the point (x1[i], y1[i]). The coordinate vectors will be recycled to the length of the longest.

Value

An object of class ADEgS.

Author(s)

Aurelie Siberchicot [email protected] and Stephane Dray

See Also

ADEg ADEgS panel.segments

Examples

data(deug, package = "ade4")
g11 <- s1d.density(deug$tab[, 1], plot = FALSE)
g12 <- addsegment(g11, x0 = deug$cent[1], x1 = deug$cent[1], y0 = 0, y1 = 1, 
  plines = list(col = "grey30", lwd = 3))
g13 <- addsegment(g11, 
  x0 = deug$cent + seq(0, 1, length.out = length(deug$cent)), 
  x1 = deug$cent + seq(0, 1, length.out = length(deug$cent)), 
  y0 = 0, y1 = 1, 
  plines = list(col = 1:length(deug$cent), lty = 1:length(deug$cent)))
  
# example extracted from the pedagogic file, here: http://pbil.univ-lyon1.fr/R/pdf/tdr65.pdf
data(monde84, package = "ade4")
dfX <- cbind.data.frame(lpib = log(monde84$pib), croipop = monde84$croipop)
dfY <- cbind.data.frame(lmorta = log(monde84$morta), lanal = log(monde84$anal + 1), 
  rscol = sqrt(100 - monde84$scol))
dfX0 <- ade4::scalewt(dfX)
dfY0 <- ade4::scalewt(dfY)
can1 <- cancor(dfX0, dfY0)
varcanoX <- dfX0 %*% can1$xcoef[,1]
varcanoY <- dfY0 %*% can1$ycoef[,1]
g21 <- s.label(cbind(varcanoY,varcanoX), labels = row.names(monde84), plabel.cex = 0.8, 
  plot = FALSE)
g22 <- addsegment(g21, -1.25, -1.25, 1.25, 1.25, plines.col = "purple", plines.lwd = 1.5, 
  plines.lty = 2)

Description

Adds a trellis object containing one or several labels on one or several graphical objects.

Usage

addtext(object, xcoord, ycoord, label, plot = TRUE, ...)

Arguments

Value

An object of class ADEgS.

Author(s)

Aurelie Siberchicot [email protected] and Stephane Dray

See Also

ADEg ADEgS adeg.panel.label

Examples

data(dunedata, package = "ade4")
afc1 <- ade4::dudi.coa(dunedata$veg, scannf = FALSE)
g1 <- table.value(dunedata$veg, symbol = "circle", ppoints.cex = 0.5, plot = FALSE)
addtext(g1, 1, 20, "A", plabels.srt = 45, plabels.box.draw = FALSE, plabels.col = "red")

xy <- cbind.data.frame(x = runif(200, -1, 1), y = runif(200, -1, 1))
posi <- factor(xy$x > 0) : factor(xy$y > 0)
g2 <- s.class(xy, fac = posi, facets = posi, pellipses.col = 1:4, plabels.cex = 0, 
  plegend.drawKey = FALSE, psub.cex = 0, plot = FALSE)
addtext(g2, c(0.5, 0.5, -0.5, -0.5), c(0.5, -0.5), levels(posi), plabels.cex = 2, plabels.col = 1:4)

Description

An object of ADEg class is a simple graphic. This object can be blended in with another one (superposition, insertion and/or juxtaposition) to form a more complex graphics (an ADEgS object).

The ADEg class is a virtual class, i.e. a class which is not possible to create objects but which have heirs. This class has five son classes : ADEg.S1, ADEg.S2, ADEg.C1, ADEg.T and ADEg.Tr.

Objects from the Class

None object of this class can be instantiated.

Slots

trellis.par

a list of parameters for lattice call. It will be passed directly to par.settings arguments of the lattice function.

adeg.par

a list of graphical parameters, corresponding to the ones given by adegpar() function.

lattice.call

a list of two elements to create the trellis object:

• graphictype: the lattice function to use

• arguments: its parameters to obtain the trellis object

g.args

a list containing some parameters linked with the created object of ADEg class:

• xlim, ylim

• main, sub

• xlab, ylab

• samelimits

• scales: a list of scales informations (ticks, marks and labels for the x-axis or the y-axis) in the form of the lattice argument scales in the xyplot function

stats

a list of internal preliminary calculations

s.misc

a list of some other internal parameters

Call

an object of class call

Methods

panelbase

signature(object = "ADEg"): draws grid and text and produces graphical output from the graphical object

getcall

signature(object = "ADEg"): returns the Call slot

getlatticecall

signature(object = "ADEg"): returns the lattice.call slot

getstats

signature(object = "ADEg"): returns the stats slot

getparameters

signature(object = "ADEg", number): if number is 1, returns the trellis.par slot, if it is 2, returns the adeg.par slot and if it is 0, returns the both slots

add.ADEg

signature(object = "ADEg"): superposes an ADEg on the current one plotted

+

signature(e1 = "ADEg", e2 = "ADEg"): superposes e2 on e1

superpose

signature(g1 = "ADEgORtrellis", g2 = "ADEgORtrellis", which = "ANY", plot = "ANY"): creates a new ADEgS object performing a superposition of g2 on g1.

printSuperpose

signature(g1 = "ADEgORtrellis", refg = "ADEgORtrellis"): internal method, not for users.

cbindADEg

signature(g1 = "ADEgORADEgS", g2 = "ADEgORADEgS"): creates a new "ADEgS" object combining g1 on g2.

rbindADEg

signature(g1 = "ADEgORADEgS", g2 = "ADEgORADEgS"): creates a new "ADEgS" object combining g1 on g2 by rows.

insert

signature(graphics = "ADEgORtrellis", oldgraphics = "missing", posi, ratio, inset, plot, which): creates a new ADEgS object performing an insertion of graphics into the current device.

insert

signature(graphics = "ADEgORtrellis", oldgraphics = "ADEg", posi, ratio, inset, plot): creates a new ADEgS object performing an insertion of graphics into oldgraphics.

show

signature(x = "ADEg"): prints the ADEg object

plot

signature(x = "ADEg"): prints the ADEg object

print

signature(x = "ADEg"): displays the ADEg object in the current device or in a new one

update

signature(object = "ADEg"): modifies graphical parameters after the ADEg creation, updates the current display and returns the modified ADEg

Note

For any ADEg creation, various graphical parameters can be passed into the dots (...) arguments.

• the parameters listed in adegpar() can be changed, even if some of them do no modify the graphic representation chosen.

• the lattice parameters listed in trellis.par.get() can also be changed.

• limits, main and sub title, and axes labels can be changed using the keys xlim, ylim, main, sub, xlab and ylab.

• a neighbouring graph (object of class nb or listw) and a spatial one (object of class sp) can be display in the background using the keys nbobject, Sp and sp.layout.

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot [email protected] and Stephane Dray

See Also

ADEgS adegpar superpose insert

Examples

showClass("ADEg")

Description

An object of ADEg.C1 class represents unidimensional data into two dimensions.

The ADEg.C1 class is a virtual class, i.e. a class which is not possible to create objects but which have heirs. This class inherits from ADEg class and has three son classes : C1.barchart, C1.curve, C1.density, C1.dotplot, C1.gauss, C1.hist, C1.interval

Objects from the Class

None object of this class can be instantiated.

Slots

data

a list containing data or data's name.

• score: the displayed values in the form of a numeric vector, a name or a matching call.

• frame: a positive or null integer. It is the number of the frame containing the data (used with sys.frame(..., env = data$frame)). Only if the data are not stored (i.e. data$storeData = FALSE).

• storeData: a logical indicating if the data should be stored in the returned object. If FALSE, only the names of the data arguments are stored.

trellis.par

a list of parameters for lattice call. It will be passed directly to par.settings arguments of the lattice function.

adeg.par

a list of graphical parameters, corresponding to the ones given by adegpar() function.

lattice.call

a list of two elements to create the trellis object:

• graphictype: xyplot

• arguments: its parameters to obtain the trellis object

g.args

a list containing some method parameters linked with the created object of ADEg.C1 class

stats

a list of internal preliminary calculations

s.misc

a list of some others internal parameters:

• hori.update: a logical indicating if the sense of direction of the graphics is updating

• backgrid: a list of two elements for grid lines. backgrid$x defines the coordinates of the lines (horizontal or vertical depending on the graphics orientation) and backgrid$d the grid mesh

Call

an object of class call

Extends

Class ADEg, directly.

Methods

prepare

signature(object = "ADEg.C1"): performs the calculations before display the object (e.g. limits, grid and axis calculations)

setlatticecall

signature(object = "ADEg.C1"): prepares the lattice.call slot

panelbase

signature(object = "ADEg.C1"): defines the graphical background (e.g. grid, rugs and box)

gettrellis

signature(object = "ADEg.C1"): converts the graphic into a trellis object of lattice class

Note

The ADEg.S1 class and ADEg.C1 class are both used to represent an unidimensional information (e.g. a score). The difference between these two classes is mainly ideological : an ADEg.S1 object is a representation into one dimension (e.g. one line) while an ADEg.C1 object is a representation into two dimensions (e.g. curves).

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot [email protected] and Stephane Dray

See Also

adegpar C1.barchart C1.curve C1.density C1.dotplot C1.gauss C1.hist C1.interval ADEg

Examples

showClass("ADEg.C1")

Description

Panel function for displaying histograms into a trellis graphic (lattice package) and level lines.

Usage

adeg.panel.hist(histValues, horizontal = TRUE, densi, drawLines, params = list(), 
  identifier = "histogramADEg")

Arguments

Value

Displays the histogram and level lines.

Note

For more information about the use of panel functions, please see the lattice package developed by Deepayan Sarkar.

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot [email protected] and Stephane Dray

See Also

bkde and hist

Examples

if(require(KernSmooth, quietly = TRUE) & require(lattice, quietly = TRUE)) {

  z <- round(rnorm(100, 30, 5))
  h <- hist(z, plot = FALSE)
  d <- bkde(z, kernel = "normal", gridsize = 60)
  l <- c(10, 20, 30, 40)
  xyplot(1:50 ~ 1:50, histValues = h, densi = d, drawLines = l, 
    panel = function(drawLines, histValues, densi){
      adeg.panel.hist(histValues = histValues, drawLines = drawLines, densi = densi)})
}

Description

Panel function for drawing lines as part of a circle centred in (0, 0) into a trellis graphic (lattice package).

Usage

adeg.panel.join(drawLines, params = list())

Arguments

Value

Displays level lines and their values.

Note

For more information about the use of panel functions, please see the lattice package developed by Deepayan Sarkar.

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot [email protected] and Stephane Dray

Examples

if(require(lattice, quietly = TRUE)) {
  xyplot(0:20 ~ 0:20, drawLines = c(5, 10, 15), params = list(plabels.cex = 2), 
    panel = function(drawLines, params){
      adeg.panel.join(drawLines = drawLines, params = params)})
}

Description

Panel function for drawing labels into a trellis graphic (lattice package) with or without boxes around labels.

Usage

adeg.panel.label(x, y, labels, plabels, pos = NULL)

Arguments

Value

Draws the labels.

Note

For more information about the use of panel functions, please see the lattice package developed by Deepayan Sarkar.

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot [email protected] and Stephane Dray

References

The algorithm used for labels positions optimization is inspired by the pointLabel function of the car package (since 2022-10-22, moved from the the maptools package, developed by Tom Short).

See Also

pointLabel

Examples

if(require(lattice, quietly = TRUE)) {
param <- adegpar("plabels")[[1]]
xyplot(1:10 ~ 1:10, panel = function(x, y, ...){
  adeg.panel.label(x, y, LETTERS[1:10], plabels = param)})
}

if(require(lattice, quietly = TRUE)) {
param$boxes$draw <- FALSE
param$col <- "blue"
xyplot(1:10 ~ 1:10, panel = function(x, y, ...){
  adeg.panel.label(x, y, LETTERS[1:10], plabels = param)})
}

Description

Panel function for representing a graph into a trellis graphic (lattice package).
Two types of graph objects can be used: nb or listw object (spdep package) or simple edges informations.
Directions associated with the edges are not displayed.

Usage

adeg.panel.nb(nbobject, coords, col.edge = "black", lwd = 1, lty = 1, pch = 20, 
  cex = 1, col.node = "black", alpha = 1)

adeg.panel.edges(edges, coords, col.edge = "black", lwd = 1, lty = 1, pch = 20, 
  cex = 1, col.node = "black", alpha = 1)

Arguments

Value

Displays the neighboring graph.

Note

For more information about the use of panel functions, please see the lattice package developed by Deepayan Sarkar.

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot [email protected] and Stephane Dray

References

Package spdep. Author: Roger Bivand

See Also

plot.nb

Examples

if(require(lattice, quietly = TRUE) &
  require(spdep, quietly = TRUE)) {

  data(elec88, package = "ade4")
  coords <- elec88$xy
  xyplot(coords[, 2] ~ coords[, 1],
    panel = function(...){adeg.panel.nb(elec88$nb, coords, col.edge = c("blue", "red"))})
}

if(require(lattice, quietly = TRUE)) {
  edges <- matrix(c(1, 2, 3, 2, 4, 1, 3, 4), byrow = TRUE, ncol = 2)
  coords <- matrix(c(0, 1, 1, 0, 0, -1, -1, 0), byrow = TRUE, ncol = 2)
  xyplot(coords[,2] ~ coords[,1],
    panel = function(...){adeg.panel.edges(edges, coords, lty = 1:4, cex = 5)})
}

Description

Panel function adapted from the Sp package for displaying all kind of spatial objects handled by Sp (for classes inherited from the superclass Spatial) into a trellis graphic (lattice package).

Usage

adeg.panel.Spatial(SpObject, sp.layout = NULL, col = 1, border = 1, lwd = 1, 
  lty = 1, alpha = 0.8, cex = 1, pch = 20, n = length(col), spIndex = 1, ...)

Arguments

Value

Draws the Spatial object and layout.

Note

If SpObject contains several maps, only the first one is selected. Also for objects containing more data (for classes data.frame with a slot data), this information is also shown. To do so, various colors can be used (according to the col arguments).

For more information about the use of panel functions, please see the lattice package developed by Deepayan Sarkar.

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot [email protected] and Stephane Dray

References

Package Sp. Author: Edzer Pebesma, Roger Bivand, Barry Rowlingson and Virgilo Gomez-Rubio.

See Also

spplot sp.lines sp.polygons sp.grid

Examples

if(require(lattice, quietly = TRUE) & require(sp, quietly = TRUE)) {
data(elec88, package = "ade4")

xy <- elec88$xy
arrow <- list("SpatialPolygonsRescale", offset = c(150000,1700000),
layout.north.arrow(), scale = 100000)

xyplot(xy[, 2] ~ xy[, 1], aspect = "iso", panel = function(...){
  adeg.panel.Spatial(SpObject = elec88$Spatial, sp.layout = list(arrow), 
  col = colorRampPalette(c("yellow", "blue"))(5), border =
  "transparent")})
}

Description

Panel function for drawing coordinates with variable representation. The values can be represented through symbols with proportional size or various colors.

Usage

adeg.panel.values(x, y, z, method, symbol, ppoints, breaks, centerpar = NULL, 
  center = 0)

Arguments

Value

Draws the points.

Note

For more information about the use of panel functions, please see the lattice package developed by Deepayan Sarkar.

For the symbols size, the method is size uses perceptual scaling (Tanimura et al. 2006).

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot [email protected] and Stephane Dray

References

Tanimura, S. and Kuroiwa, C. and Mizota, T. 2006 Proportional symbol mapping in R Journal of Statistical Software 15, 1–7

Examples

if(require(lattice, quietly = TRUE)) {
param <- adegpar("ppoints")[[1]]
param$col <- adegpar("ppalette")[[1L]]$quanti(2)
z <- rnorm(10)
xyplot(1:10 ~ 1:10, panel = function(x, y, ...){
  adeg.panel.values(x, y, z, method = "size", symbol = "square", ppoints =
  param, breaks = pretty(z, 4))})
}

if(require(lattice, quietly = TRUE)) {
param$col <- adegpar()$ppalette$quali((length(pretty(z, 2)) - 1))
xyplot(1:10 ~ 1:10, panel = function(x, y, ...){
  adeg.panel.values(x, y, z, method = "color", symbol = "circle", 
                    ppoints = param, breaks = pretty(z, 2))}) 
}

Description

An object of ADEg.S1 class represents unidimensional data into one dimension.

The ADEg.S1 class is a virtual class, i.e. a class which is not possible to create objects but which have heirs. This class inherits from ADEg class and has five son classes : S1.boxplot, S1.class, S1.distri, S1.label and S1.match.

Objects from the Class

None object of this class can be instantiated.

Slots

data

a list containing data or data's name.

• score: the displayed values in the form of a numeric vector, a name or a matching call.

• at: the index value.

• frame: a positive or null integer. It is the number of the frame containing the data (used with sys.frame(..., env = data$frame)). Only if the data are not stored (i.e. data$storeData = FALSE).

• storeData: a logical indicating if the data should be stored in the returned object. If FALSE, only the names of the data arguments are stored.

trellis.par

a list of parameters for lattice call. It will be passed directly to par.settings arguments of the lattice function.

adeg.par

a list of graphical parameters, corresponding to the ones given by adegpar() function.

lattice.call

a list of two elements to create the trellis object:

• graphictype: xyplot

• arguments: its parameters to obtain the trellis object

g.args

a list containing some method parameters linked with the created object of ADEg.S1 class.

stats

a list of internal preliminary calculations

s.misc

a list of some others internal parameters:

• hori.update: a logical indicating if the sense of direction of the graphics is updating

• backgrid: a list of two elements for grid lines. backgrid$x defines the coordinates of the lines (horizontal or vertical depending on the graphics orientation) and backgrid$d the grid mesh

• rug: an index value indicating where the rugs are drawn

Call

an object of class call

Extends

Class ADEg, directly.

Methods

prepare

signature(object = "ADEg.S1"): performs the calculations before display the object (e.g. limits, grid and axis calculations)

setlatticecall

signature(object = "ADEg.S1"): prepares the lattice.call slot

panelbase

signature(object = "ADEg.S1"): defines the graphical background (e.g. grid, rugs and box)

gettrellis

signature(object = "ADEg.S1"): converts the graphic into a trellis object of lattice class

zoom

signature(object = "ADEg.S1", zoom = "numeric", center = "missing"): performs a zoom in (if zoom < 1) or out (if zoom > 1) centered, only in one-dimension

zoom

signature(object = "ADEg.S1", zoom = "numeric", center = "numeric"): performs a zoom in (if zoom < 1) or out (if zoom > 1) around the center passed in parameter, only in one-dimension

Note

Various graphical parameters are used for display an ADEg.S1 object. The list p1d in adegpar() is thought specific for ADEg.S1 objects.

The ADEg.S1 class and ADEg.C1 class are both used to represent an unidimensional information (e.g. a score). The difference between these two classes is mainly ideological : an ADEg.S1 object is a representation into one dimension (e.g. one line) while an ADEg.C1 object is a representation into two dimensions (e.g. curves).

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot [email protected] and Stephane Dray

See Also

adegpar zoom S1.boxplot S1.class S1.distri S1.label S1.match ADEg

Examples

showClass("ADEg.S1")
adegpar("p1d")

Description

An object of ADEg.S2 class represents bi-dimensional data.

The ADEg.S2 class is a virtual class, i.e. a class which is not possible to create objects but which have heirs. This class inherits from ADEg class and has eleven son classes : S2.arrow, S2.class, S2.corcircle, S2.density, S2.distri, S2.image, S2.label, S2.logo, S2.match, S2.traject and S2.value.

Objects from the Class

None object of this class can be instantiated.

Slots

data

a list containing data or data's name.

• dfxy: the displayed values in the form of a data frame, a name or a matching call.

• xax: an integer or a vector indicating the columns of dfxy kept for the x-axes.

• yax: an integer or a vector indicating the columns of dfxy kept for the y-axes.

• frame: a positive or null integer. It is the number of the frame containing the data (used with sys.frame(..., env = data$frame)). Only if the data are not stored (i.e. data$storeData = FALSE).

• storeData: a logical indicating if the data should be stored in the returned object. If FALSE, only the names of the data arguments are stored.

trellis.par

a list of parameters for lattice call. It will be passed directly to par.settings arguments of the lattice function.

adeg.par

a list of graphical parameters, corresponding to the ones given by adegpar() function.

lattice.call

a list of two elements to create the trellis object:

• graphictype: xyplot

• arguments: its parameters to obtain the trellis object

g.args

a list containing some method parameters linked with the created object of ADEg.S2 class:

• fullcircle: only for S2.corcircle objects

• method: only for S2.value objects

• symbol: only for S2.value objects

• center: only for S2.value objects

stats

a list of internal preliminary calculations

s.misc

a list of some others internal parameters:

• xfullcircle.update and yfullcircle.update: a logical indicating if the circle size is updating (only for S2.corcircle objects)

• plegend.update: a logical indicating if the legend parameters are updating

• breaks.update: a logical indicating if the legend breaks are updating

• backgrid: a list of elements for grid lines

Call

an object of class call

Extends

Class ADEg, directly.

Methods

prepare

signature(object = "ADEg.S2"): performs the calculations before display the object (e.g. limits, grid and axis calculations)

setlatticecall

signature(object = "ADEg.S2"): prepares the lattice.call slot

panelbase

signature(object = "ADEg.S2"): defines the graphical background (e.g. grid and box)

gettrellis

signature(object = "ADEg.S2"): converts the graphic into a trellis object of lattice class

zoom

signature(object = "ADEg.S2", zoom = "numeric", center = "missing"): performs a zoom in (if zoom < 1) or out (if zoom > 1) centered

zoom

signature(object = "ADEg.S2", zoom = "numeric", center = "numeric"): performs a zoom in (if zoom < 1) or out (if zoom > 1) around the center passed in parameter (center should be a two-length vector)

addhist

signature(object = "ADEg.S2"): adds histograms and density lines against a bi-dimensional graphics

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot [email protected] and Stephane Dray

See Also

addhist zoom adegpar S2.arrow S2.class S2.corcircle S2.density S2.distri S2.image S2.label S2.logo S2.match S2.traject S2.value ADEg

Examples

showClass("ADEg.S2")

Description

An object of ADEg.T class represents table data.

The ADEg.T class is a virtual class, i.e. a class which is not possible to create objects but which have heirs. This class inherits from ADEg class and has two son classes : T.image and T.value.

Objects from the Class

None object of this class can be instantiated.

Slots

data:

a list containing data or data's name.

• dftab: the displayed values which can be table, dist or matrix in the form of a data frame, a name or a matching call

• coordsx: an integer or a vector indicating the columns of dftab kept

• coordsy: an integer or a vector indicating the rows of dftab kept

• labelsx: the columns' labels

• labelsy: the rows' labels

• "frame: a positive or null integer. It is the number of the frame containing the data (used with sys.frame(..., env = data$frame)). Only if the data are not stored (i.e. data$storeData = FALSE).

• storeData: a logical indicating if the data should be stored in the returned object. If FALSE, only the names of the data arguments are stored.

trellis.par

a list of parameters for lattice call. It will be passed directly to par.settings arguments of the lattice function.

adeg.par

a list of graphical parameters, corresponding to the ones given by adegpar() function.

lattice.call

a list of two elements to create the trellis object:

• graphictype: xyplot

• arguments: its parameters to obtain the trellis object

g.args

a list containing some method parameters linked with the created object of ADEg.T class:

• method: only for T.value objects

• symbol: only for T.value objects

• center: only for T.value objects

stats

a list of internal preliminary calculations

s.misc

a list of some others internal parameters:

• breaks.update: a logical indicating if the legend breaks is updating

• axes$dx and axes$dy: intervals for the cell size

Call

an object of class call

Extends

Class ADEg, directly.

Methods

prepare

signature(object = "ADEg.T"): performs the calculations before display the object (e.g. limits, grid and axis calculations)

setlatticecall

signature(object = "ADEg.T"): prepares the lattice.call slot

panelbase

signature(object = "ADEg.T"): defines the graphical background (e.g. axes, labels, ticks, box and grid)

gettrellis

signature(object = "ADEg.T"): converts the graphic into a trellis object of lattice class

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot [email protected] and Stephane Dray

See Also

adegpar T.image T.value ADEg

Examples

showClass("ADEg.T")

Description

An object of ADEg.Tr class represents triangular coordinates in 2D.

The ADEg.Tr class is a virtual class, i.e. a class which is not possible to create objects but which have heirs. This class inherits from ADEg class and has three son classes : Tr.class, Tr.label, T.match and T.traject.

Objects from the Class

None object of this class can be instantiated.

Slots

data:

a list containing data or data's name.

• dfxyz: the displayed values in the form of a data frame with three columns, a name or a matching call.

• frame: a positive or null integer. It is the number of the frame containing the data (used with sys.frame(..., env = data$frame)). Only if the data are not stored (i.e. data$storeData = FALSE).

• storeData: a logical indicating if the data should be stored in the returned object. If FALSE, only the names of the data arguments are stored.

trellis.par

a list of parameters for lattice call. It will be passed directly to par.settings arguments of the lattice function.

adeg.par

a list of graphical parameters, corresponding to the ones given by adegpar() function.

lattice.call

a list of two elements to create the trellis object:

• graphictype: xyplot

• arguments: its parameters to obtain the trellis object

g.args

a list containing some method parameters linked with the created object of ADEg.Tr class:

• max3d and min3d: triangular limits

• adjust: a logical to adjust the device with the limits

stats

a list of internal preliminary calculations

s.misc

a list of some others internal parameters:

• adjust.update: a logical indicating if the adjust slot is updating

• cornerp: coordinates of the triangle extremities.

• lgrid: a list containing the three coordinates of the grid segments extremities(pts1, pts2, pts3) and the value of the division (posgrid)

Call

an object of class call

Extends

Class ADEg, directly.

Methods

prepare

signature(object = "ADEg.Tr"): performs the calculations before display the object (e.g. limits, grid and axis calculations)

setlatticecall

signature(object = "ADEg.Tr"): prepares the lattice.call slot

panelbase

signature(object = "ADEg.Tr"): defines the graphical background (e.g. triangle and grid)

gettrellis

signature(object = "ADEg.Tr"): converts the graphic into a trellis object of lattice class

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot [email protected] and Stephane Dray

See Also

adegpar Tr.class Tr.label Tr.match Tr.traject ADEg

Examples

showClass("ADEg.Tr")

Description

adegpar can be used to set or query graphical parameters used in ADEg object display.

It is inspired by the par function of graphics package.

Usage

adegpar(...)

Arguments

Details

The graphical parameters control apparency of the graphic. Calls can be made using either a list of list (e.g. plabels = list(col = "red")) or a list grouping both keys with "." (e.g. plabels.col = "red").

Parameters are re-used if needed in all ADEg object. If set globally, meaning using adegpar, all created objects afterwards will be affected.

Value

Several parameters are used to create complete plot and accessible through adegpar.

p1d:

parameters for one-dimension graphic, object of class inherited from "ADEg.S1" or "ADEg.C1"

• horizontal: a logical indicating if the plot is horizontal

• reverse: a logical indicating if the bottom of the plot is at the bottom (for horizontal as TRUE) or at the left of the device (for horizontal as FALSE). If FALSE, the graphical display bottom is at the top (for horizontal as TRUE) or at the right of the device (for horizontal as FALSE).

• rug: a list dedicated to tick marks

  • draw: a logical indicating if the rugs are drawn

  • tck: size of the rug (ticks) in proportion from the reference line and the origin of the device (0.5 by default)

  • margin: where to draw the reference line (0.07 by default)

  • line: a logical indicating if the reference line is drawn using porigin arguments

parrows:

arrows' parameters. see panel.arrows for more information

• angle: angle from the shaft of the arrow to the edge of the arrow head

• ends: kind of arrows to be drawn. Can be first, last or both

• length: length of the edges of the arrow head

paxes:

axis' parameters. Mostly inspired by xyplot function of lattice package

• aspectratio: a character string to control physical aspect ratio of the graphic (drawing panel more specifically). iso for isometric scales, fill for drawing as big as possible or xy for banking rule

• draw: a logical indicating if axis (tick marks and labels) are drawn around the graphic

• x: a list used for the creation of x-axis in the trellis object. See xyplot for more information

  • draw: a logical indicating if x-axis (tick marks and labels) are drawn around the graphic

• y: the same list as for x with draw parameters

pbackground:

background's parameters

• col: background color

• box: a logical indicating if a box is drawn surrounding the plot

pellipses:

ellipses' drawing parameters

• alpha: a value between 0 and 1 controlling ellipses' background transparency

• axes: a list dedicated to ellipses' axis

  • draw: a logical indicating whether ellipses' axis are drawn

  • col: ellipses' axis color

  • lty: line type of ellipses' axis

  • lwd: line width of ellipses' axis

• border: ellipses's border color

• lty: line type of ellipses' border

• lwd: line width of ellipses' border

• col: ellipses' background color

pgrid:

grid's drawing parameters

• draw: a logical indicating if grid is drawn in the background

• col: grid's line color

• lty: line type of grid line

• lwd: line width of grid line

• nint: an integer indicating the number of grid intervals expected

• text: a list dedicated to grid legend text

  • cex: text size of grid legend

  • col: text color of grid legend

  • pos: a character string (topright, topleft, bottomleft, bottomright) or a vector of length 2 indicating text position of grid legend. If it is a vector, the default unit is npc (normalized parent coordinates).

plabels:

labels' drawing parameters

• alpha: a value between 0 and 1 controlling label transparency

• cex: labels' text size

• col: labels' text color

• srt: labels' text orientation. It can be horizontal, vertical or an angle indication in degrees

• optim: a logical indicating if an algorithm is used to avoid labels' overlapping or outside limits

• boxes: label's boxes parameters

  • draw: a logical indicating if labels are framed

  • alpha: a value between 0 and 1 controlling labels' boxes transparency

  • border: boxes' border color

  • col: boxes' background color

  • lty: line type of boxes' border

  • lwd: line width of boxes' border

plegend:

legend's drawing parameters (used for object of class inherited from T.value and S2.value)

• drawKey: a logical indicating if the legend should be drawn. Legend can be provided by the key argument or is automatically generated for *.class and *.value functions

• drawColorKey: a logical indicating if the color legend should be drawn (only for *.image functions)

• size: size of the legend

plines:

lines' drawing parameters

• col: lines color

• lty: lines type

• lwd: lines width

pnb:

drawing parameters for neighbourhood graph

• edge: edge's drawing parameters

  • col: edge color

  • lty: line type of edge

  • lwd: line width of edge

• node: node's drawing parameters

  • pch: node's symbol type

  • cex: node's symbol size

  • col: node's symbol color

  • alpha: a value between 0 and 1 controlling node's symbol transparency

porigin:

drawing parameters for origin's lines. See panel.lines for more information

• draw: a logical indicating if vertical and horizontal lines are drawn to indicate origin

• include: a logical indicating if origin is included in the drawing limits

• origin: a two-length vector indicating origin coordinates

• alpha: a value between 0 and 1 controlling origin's lines transparency

• col: color of origin's lines

• lty: origin's line type

• lwd: origin's line width

ppalette:

a function taking one integer in argument indicating the number of expecting colors (for example using colorRampPalette)

• quanti: adegpar()$ppalette$quanti(n) returns n colors shaded grey to white

• quali: adegpar()$ppalette$quali(n, name) returns n differentiated colors. name argument is passed to the brewer.pal function of the RColorBrewer package and must be Accent, Dark2, Paired, Pastel1, Pastel2, Set1 (the default value), Set2 or Set3. When n is equal to 2, values for 'white' and 'black' colors are returned and can be not quite visible on the display.

ppoints:

points' drawing paameters

• alpha: a value between 0 and 1 controlling points transparency

• cex: points size

• col: points color

• pch: points type

• fill: points' background color (only for filled points type)

ppolygons:

polygons' drawing parameters (used for example to draw convex hull for S2.class or Gaussian curves for C1.gauss objects). See lpolygon for more information.

• border: polygon's border color

• col: polygon's background color

• lty: line type of polygon border

• lwd: line width of polygon border

• alpha: a value between 0 and 1 controlling polygons' background transparency

pSp:

drawing parameters for spatial object

• col: spatial object's background color

• border: spatial object's border color

• lty: line type of spatial object border

• lwd: line width of spatial object border

• alpha: a value between 0 and 1 controlling spatial object transparency

psub:

subtitle's drawing parameters

• cex: text size of subtitle

• col: text color of subtitle

• position: a character string (topright, topleft, bottomleft, bottomright) or a vector of length 2 indicating text position of subtitle. If it is a vector, the default unit is npc (normalized parent coordinates).

• text: the character string to display

ptable:

for table graphic, object of class inherited from ADEg.T

• x: x-axis parameters

  • srt: text rotation

  • pos: position of the axis. It can be top or bottom. Otherwise axis and labels' axis are not drawn

  • tck: ticks size

  • adj: justification of labels

• y: same as x list, but for y-axis

  • str, tck, adj

  • pos: position of the axis. It can be left or right. Otherwise axis and labels' axis are not drawn

• margin: margin surrounding the drawing panel. The numbers indicate the bottom, left, top and right margins. Results are obtained passing margin to padding argument in lattice. Please see layout.heights and layout.widths parameters in lattice package for more information

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot [email protected] and Stephane Dray

See Also

ADEg par

Examples

oldparamadeg <- adegpar()
    
X <- data.frame(x = runif(50, -1, 2), y = runif(50, -1, 2))
s.label(X)
names(adegpar())
adegpar("paxes.draw", "psub.cex")
adegpar()$pback$col
adegpar("paxes.draw" = TRUE, "psu.ce" = 3, "pback.col" = "grey85")
s.label(X)

adegpar(oldparamadeg)

Description

Creates and displays an "ADEgS" object, a set of ADEg, trellis and/or ADEgS objects, managed by superposition, insertion and/or juxtaposition.

Usage

ADEgS(adeglist, positions, layout, add = NULL, plot = TRUE)

Arguments

Value

an ADEgS object. If plot = TRUE, the created object is displayed.

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot [email protected] and Stephane Dray

See Also

ADEgS

Examples

xy <- matrix(rnorm(20), ncol = 2)
g1 <- s.label(xy)
g2 <- s.class(xy, fac = as.factor(rep(LETTERS[1:2], length.out = 10)), ppoints.cex = 0,
  col = c("blue", "red"))
g3 <- ADEgS(list(g1, g2), rbind(c(0, 0, 0.5, 1), c(0.5, 0, 1, 1)))
g4 <- ADEgS(list(g1, g2), layout = c(2, 1))
g5 <- ADEgS(list(g1, g2))
g6 <- ADEgS(list(g1, g2), add = matrix(c(0, 1, 0, 0), byrow = TRUE, ncol = 2))

data(olympic, package = "ade4")
dudi1 <- ade4::dudi.pca(olympic$tab, scan = FALSE)
g7 <- s.arrow(dudi1$li)
g8 <- s.corcircle(dudi1$co, lab = names(olympic$tab))
g9 <- ADEgS(list(g7, g8), rbind(c(0, 0, 0.5, 1), c(0.5, 0, 1, 1)))
g9[[1]]
g9[1, drop = FALSE]
length(g9)

Description

An object of ADEgS class is a complex graphic. This class allows the superposition, the insertion and/or the juxtaposition of several ADEg, trellis and/or ADEgS objects.

The ADEgS class have neither father class nor son classes.

Objects from the Class

ADEgS objects can be created by calls of the form new("ADEgS", ...).

The regular usage in this package is to use the ADEgS, add.ADEg, superpose, insert or + functions.

Slots

ADEglist

a list of several trellis, ADEg and/or ADEgS objects.

positions

a matrix with four columns and as many rows as the number of graphical objects in the ADEglist slot. For each simple graphic, i.e. in each row, the coordinates of the top-right and the bottom-left hand corners are in npc unit (normalized parent coordinates).

add

a square matrix with as many rows and columns as the number of graphical objects in the ADEglist slot. The value at the i-th row and j-th column is equal to 1 whether the j-th graphical object in the ADEglist slot is superpose to i-th graphical one. Otherwise, this value is equal to 0.

Call

an object of class call

Methods

[

signature(x = "ADEgS", i = "numeric", j = "missing", drop = "logical"): extracts the i-th sub-graphics in the x@ADEglist. i can be a vector. If i is a single number and if the extracted graphic in an ADEg object, the sub-selection is in the form of ADEg if drop is TRUE and in the form of ADEgS otherwise.

[

signature(x = "ADEgS", i = "numeric", j = "missing", drop = "missing"): the same than the previous method. drop is FALSE by default

[[

signature(x = "ADEgS", i = "numeric", j = "missing"): extracts one sub-graphic, the i-th one, in the x@ADEglist

[[

signature(x = "ADEgS", i = "character", j = "missing"): extracts one sub-graphic, named i in the x@ADEglist

[[<-

signature(x = "ADEgS", i = "numeric", j = "missing", value = "ADEg"): replaces one sub graphic, the i-th one, by an ADEg object in the x@ADEglist

[[<-

signature(x = "ADEgS", i = "numeric", j = "missing", value = "ADEgS"): replaces one sub graphic, the i-th one, by an ADEgS object in the x@ADEglist

$

signature(x = "ADEgS"): extracts one sub-graphic by its name in the x@ADEglist

getpositions

signature(object = "ADEgS"): returns the positions matrix of the object, i.e. object@positions

getgraphics

signature(object = "ADEgS"): returns the list of graphics of the object, i.e. object@ADEglist

getcall

signature(object = "ADEgS"): returns the call of the object, i.e. object@Call

names

signature(object = "ADEgS"): returns the graphics' names of the object, i.e. the names of object@ADEglist

names<-

signature(object = "ADEgS"): replaces the graphics' names of the object, i.e. the names of object@ADEglist

length

signature(x = "ADEgS"): returns the number of graphics into x, i.e. the length of x@ADEglist

plot

signature(x = "ADEgS"): same as print

print

signature(x = "ADEgS"): displays the graphical elements into one device using positions and superposition management (x@add matrix)

show

signature(object = "ADEgS"): same as print

superpose

signature(g1 = "ADEgS", g2 = "ADEg", which = "numeric", plot = "logical"): creates a new "ADEgS" object performing a superposition of g2 on the which-th ADEg object of g1. This object is printed if plot is TRUE.

superpose

signature(g1 = "ADEgS", g2 = "ADEg", which = "numeric", plot = "ANY"): creates a new "ADEgS" object performing a superposition of g2 on the which-th ADEg object of g1. This object is printed only if plot is TRUE.

superpose

signature(g1 = "ADEgS", g2 = "ADEg", which = "missing", plot = "ANY"): creates a new "ADEgS" object performing a superposition of g2 on the last ADEg object of g1. This object is printed only if plot is TRUE.

superpose

signature(g1 = "ADEgS", g2 = "ADEgS", which = "missing", plot = "ANY"): creates a new "ADEgS" object performing a superposition between two ADEgS having the same length and the same positions slot. It is used when g1 and g2 are both created with a partition of individual groups, variables or analysis' axis.

+

signature(e1 = "ADEg", e2 = "ADEgS"): creates a new "ADEgS" object performing a superposition of e1 on e2.

+

signature(e1 = "ADEgS", e2 = "ADEg"): creates a new "ADEgS" object performing a superposition of e2 on e1.

cbindADEg

signature(g1 = "ADEgORADEgS", g2 = "ADEgORADEgS"): creates a new "ADEgS" object combining g1 on g2 by columns.

rbindADEg

signature(g1 = "ADEgORADEgS", g2 = "ADEgORADEgS"): creates a new "ADEgS" object combining g1 on g2 by rows.

update

signature(object = "ADEgS"): modifies the graphical parameters of each sub-graphics listed in object@ADEglist and/or the object's names (with the key word names) and/or the object@positions slot (with the key word positions), after creation of the object. The current display is updated and a modified object is returned.

insert

signature(graphics = "ADEgS", oldgraphics = "missing", posi, ratio, inset, plot, which, dispatch): creates a new "ADEgS" object performing an insertion of graphics into the current device.

insert

signature(graphics = "ADEgS", oldgraphics = "ADEg", posi, ratio, inset, plot): creates a new "ADEgS" object performing an insertion of graphics into oldgraphics.

insert

signature(graphics = "ADEgORtrellis", oldgraphics = "ADEgS", posi, ratio, inset, plot, which): creates a new "ADEgS" object performing an insertion of graphics into oldgraphics.

insert

signature(graphics = "ADEgS", oldgraphics = "ADEgS", posi, ratio, inset, plot, which, dispatch): creates a new "ADEgS" object performing an insertion of graphics into oldgraphics.

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot [email protected] and Stephane Dray

See Also

ADEg ADEgS superpose insert

Examples

showClass("ADEgS")

Description

A class for the creation and display of a numeric score using barcharts.

Objects from the Class

C1.barchart objects can be created by calls of the form new("C1.barchart", ...).

The regular usage in this package is to use the s1d.barchart function.

Slots

data

a list containing data or data's name.

• score: the displayed values in the form of a vector, a factor, a name or a matching call.

• labels: the labels' names drawn on the top of bars.

• at: the index value.

• frame: a positive or null integer. It is the number of the frame containing the data (used with sys.frame(..., env = data$frame)). Only if the data are not stored (i.e. data$storeData = FALSE).

• storeData: a logical indicating if the data should be stored in the returned object. If FALSE, only the names of the data arguments are stored.

trellis.par

a list of parameters for lattice call. It will be passed directly to par.settings arguments of the lattice function.

adeg.par

a list of graphical parameters, corresponding to the ones given by adegpar() function.

lattice.call

a list to create the trellis object.

g.args

a list containing some method parameters linked with the created object of ADEg.C1 class. The specific slot for C1.barchart objects is:

• sort: a logical indicating if score is sorted in ascending order.

stats

a list of internal preliminary calculations

s.misc

a list of some others internal parameters

Call

an object of class call

Extends

Class ADEg.C1, directly.
Class ADEg, by class ADEg.C1, distance 2.
Class ADEgORtrellis, by class ADEg.C1, distance 3.
Class ADEgORADEgSORtrellis, by class ADEg.C1, distance 3.

Methods

The methods of the father classes "ADEg.C1" and "ADEg" can be used by inheritance. The specific methods for C1.barchart are:

prepare

signature(object = "C1.barchart"): calls the parent method (prepare for ADEg.C1) and modifies some graphical parameters used by default.

panel

signature(object = "C1.barchart"): draws bar charts and labels.

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot [email protected] and Stephane Dray

See Also

ADEg ADEg.C1 s1d.barchart

Examples

showClass("C1.barchart")

Description

A class for the creation and display of a numeric score linked by curves. The C1.curves allows to deal with multiple scores.

Objects from the Class

C1.curve objects can be created by calls of the form new("C1.curve", ...). The regular usage in this package is to use the s1d.curve function.

C1.curves objects can be created by calls of the form new("C1.curves", ...). The regular usage in this package is to use the s1d.curves function. Class C1.curves extends C1.curve directly.

Slots

data

a list containing data or data's name.

• score: the displayed values in the form of a vector, a factor, a name or a matching call.

• at: the index value.

• frame: a positive or null integer. It is the number of the frame containing the data (used with sys.frame(..., env = data$frame)). Only if the data are not stored (i.e. data$storeData = FALSE).

• storeData: a logical indicating if the data should be stored in the returned object. If FALSE, only the names of the data arguments are stored.

trellis.par

a list of parameters for lattice call. It will be passed directly to par.settings arguments of the lattice function.

adeg.par

a list of graphical parameters, corresponding to the ones given by adegpar() function.

lattice.call

a list to create the trellis object.

g.args

a list containing some method parameters linked with the created object of ADEg.C1 class.

stats

a list of internal preliminary calculations

s.misc

a list of some others internal parameters

Call

an object of class call

Extends

Class ADEg.C1, directly.
Class ADEg, by class ADEg.C1, distance 2.
Class ADEgORtrellis, by class ADEg.C1, distance 3.
Class ADEgORADEgSORtrellis, by class ADEg.C1, distance 3.

Methods

The methods of the father classes "ADEg.C1" and "ADEg" can be used by inheritance. The specific methods for C1.curve and C1.curves are:

prepare

signature(object = "C1.curve"): calls the parent method (prepare for ADEg.C1) and modifies some graphical parameters used by default.

panel

signature(object = "C1.curve"): draws points and curves.

panel

signature(object = "C1.curves"): draws points and curves.

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot [email protected] and Stephane Dray

See Also

ADEg ADEg.C1 s1d.curve s1d.curves

Examples

showClass("C1.curve")
showClass("C1.curves")

Description

A class for the creation and display of a numeric score using density curves.

Objects from the Class

C1.density objects can be created by calls of the form new("C1.density", ...).

The regular usage in this package is to use the s1d.density function.

Slots

data

a list containing data or data's name.

• score: the displayed values in the form of a numeric vector, a name or a matching call.

• fac: a factor for score to split in the form of a vector, a factor, a name or a matching call.

• frame: a positive or null integer. It is the number of the frame containing the data (used with sys.frame(..., env = data$frame)). Only if the data are not stored (i.e. data$storeData = FALSE).

• storeData: a logical indicating if the data should be stored in the returned object. If FALSE, only the names of the data arguments are stored.

trellis.par

a list of parameters for lattice call. It will be passed directly to par.settings arguments of the lattice function.

adeg.par

a list of graphical parameters, corresponding to the ones given by adegpar() function.

lattice.call

a list to create the trellis object.

g.args

a list containing some method parameters linked with the created object of ADEg.C1 class. The specific slots for C1.density objects are:

• kernel, bandwidth and gridsize: passed in parameters in bkde function of the KernSmooth package.

• fill: a logical to yield the polygons density curves filled.

• col: a logical, a color or a colors vector to color labels, rugs, lines and polygons.

stats

a list of internal preliminary calculations. The specific slot for C1.density objects is:

• densit: the values of density curve calculated for each factor in fac computes with the bkde function of the KernSmooth package.

s.misc

a list of some others internal parameters. The specific slot for C1.density objects is:

• rug: an index value indicating where the rugs are drawn

Call

an object of class call

Extends

Class ADEg.C1, directly.
Class ADEg, by class ADEg.C1, distance 2.
Class ADEgORtrellis, by class ADEg.C1, distance 3.
Class ADEgORADEgSORtrellis, by class ADEg.C1, distance 3.

Methods

The methods of the father classes "ADEg.C1" and "ADEg" can be used by inheritance. The specific methods for C1.density are:

prepare

signature(object = "C1.density"): calls the parent method (prepare for ADEg.C1), modifies some graphical parameters used by default and calculates the density curves according to the numeric score and the values' categories.

panel

signature(object = "C1.density"): draws density curves.

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot [email protected] and Stephane Dray

See Also

ADEg ADEg.C1 s1d.density

Examples

showClass("C1.density")

Description

A class for the creation and display of a numeric score using dots.

Objects from the Class

C1.dotplot objects can be created by calls of the form new("C1.dotplot", ...).

The regular usage in this package is to use the s1d.dotplot function.

Slots

data

a list containing data or data's name.

• score: the displayed values in the form of a vector, a factor, a name or a matching call.

• at: the index value.

• frame: a positive or null integer. It is the number of the frame containing the data (used with sys.frame(..., env = data$frame)). Only if the data are not stored (i.e. data$storeData = FALSE).

• storeData: a logical indicating if the data should be stored in the returned object. If FALSE, only the names of the data arguments are stored.

trellis.par

a list of parameters for lattice call. It will be passed directly to par.settings arguments of the lattice function.

adeg.par

a list of graphical parameters, corresponding to the ones given by adegpar() function.

lattice.call

a list to create the trellis object.

g.args

a list containing some method parameters linked with the created object of ADEg.C1 class.

stats

a list of internal preliminary calculations

s.misc

a list of some others internal parameters

Call

an object of class call

Extends

Class ADEg.C1, directly.
Class ADEg, by class ADEg.C1, distance 2.
Class ADEgORtrellis, by class ADEg.C1, distance 3.
Class ADEgORADEgSORtrellis, by class ADEg.C1, distance 3.

Methods

The methods of the father classes "ADEg.C1" and "ADEg" can be used by inheritance. The specific methods for C1.dotplot are:

prepare

signature(object = "C1.dotplot"): calls the parent method (prepare for ADEg.C1) and modifies some graphical parameters used by default.

panel

signature(object = "C1.dotplot"): draws segments and dots.

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot [email protected] and Stephane Dray

See Also

ADEg ADEg.C1 s1d.dotplot

Examples

showClass("C1.dotplot")

Description

A class for the creation and display of a numeric score using gauss' curves.

Objects from the Class

C1.gauss objects can be created by calls of the form new("C1.gauss", ...).

The regular usage in this package is to use the s1d.gauss function.

Slots

data

a list containing data or data's name.

• score: the displayed values in the form of a numeric vector, a name or a matching call.

• fac: a factor for score splitting in the form of a vector, a factor, a name or a matching call.

• wt: a vector of weights for score

• frame: a positive or null integer. It is the number of the frame containing the data (used with sys.frame(..., env = data$frame)). Only if the data are not stored (i.e. data$storeData = FALSE).

• storeData: a logical indicating if the data should be stored in the returned object. If FALSE, only the names of the data arguments are stored.

trellis.par

a list of parameters for lattice call. It will be passed directly to par.settings arguments of the lattice function.

adeg.par

a list of graphical parameters, corresponding to the ones given by adegpar() function.

lattice.call

a list to create the trellis object.

g.args

a list containing some method parameters linked with the created object of ADEg.C1 class. The specific slots for C1.gauss objects are:

• fill: a logical to yield the gauss curves transparent.

• col: a logical, a color or a colors vector to color labels, rugs, lines and polygons.

• steps: a value for the number of segments used to draw Gauss curves.

stats

a list of internal preliminary calculations. The specific slots for C1.gauss objects are:

• means: the weighted mean calculated for each fac value.

• var: the weighted variance calculated for each fac value.

• gausscurves: the density gauss curve calculated for each fac value.

s.misc

a list of some others internal parameters. The specific slot for C1.gauss objects is:

• rug: an index value indicating where the rugs are drawn

Call

an object of class call

Extends

Class ADEg.C1, directly.
Class ADEg, by class ADEg.C1, distance 2.
Class ADEgORtrellis, by class ADEg.C1, distance 3.
Class ADEgORADEgSORtrellis, by class ADEg.C1, distance 3.

Methods

The methods of the father classes "ADEg.C1" and "ADEg" can be used by inheritance. The specific methods for C1.gauss are:

prepare

signature(object = "C1.gauss"): calls the parent method (prepare for ADEg.C1), modifies some graphical parameters used by default and calculates the Gauss curves according to the numeric score and the values' categories (using weighted mean and standard deviation).

panel

signature(object = "C1.gauss"): draws Gauss curves and level names of each curve.

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot [email protected] and Stephane Dray

See Also

ADEg ADEg.C1 s1d.gauss

Examples

showClass("C1.gauss")

Description

A class for the creation and display of a numeric score using a histogram.

Objects from the Class

C1.hist objects can be created by calls of the form new("C1.hist", ...).

The regular usage in this package is to use the s1d.hist function.

Slots

data

a list containing data or data's name.

• score: the displayed values in the form of a vector, a factor, a name or a matching call.

• frame: a positive or null integer. It is the number of the frame containing the data (used with sys.frame(..., env = data$frame)). Only if the data are not stored (i.e. data$storeData = FALSE).

• storeData: a logical indicating if the data should be stored in the returned object. If FALSE, only the names of the data arguments are stored.

trellis.par

a list of parameters for lattice call. It will be passed directly to par.settings arguments of the lattice function.

adeg.par

a list of graphical parameters, corresponding to the ones given by adegpar() function.

lattice.call

a list to create the trellis object.

g.args

a list containing some method parameters linked with the created object of ADEg.C1 class. The specific slots for C1.hist objects are:

• breaks: a vector of values to split score. If NULL, pretty(score, nclass) is used.

• nclass: an integer for the number of desired intervals, ignored if breaks is not missing.

• type: a value among count, density, percent to indicate the unit of the cell height.

• right: a logical indicating if the histogram cells are right-closed (left open) intervals.

stats

a list of internal preliminary calculations. The specific slots for C1.hist objects are:

• heights: the cell height.

• breaks: the cell boundaries.

s.misc

a list of some others internal parameters

Call

an object of class call

Extends

Class ADEg.C1, directly.
Class ADEg, by class ADEg.C1, distance 2.
Class ADEgORtrellis, by class ADEg.C1, distance 3.
Class ADEgORADEgSORtrellis, by class ADEg.C1, distance 3.

Methods

The methods of the father classes "ADEg.C1" and "ADEg" can be used by inheritance. The specific methods for C1.hist are:

prepare

signature(object = "C1.hist"): calls the parent method (prepare for ADEg.C1), modifies some graphical parameters used by default and calculates the boundaries and the height of cells.

panel

signature(object = "C1.hist"): draws rectangles.

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot [email protected] and Stephane Dray

See Also

ADEg ADEg.C1 s1d.hist

Examples

showClass("C1.hist")

Description

A class for the creation and display of an interval between two numeric scores.

Objects from the Class

C1.interval objects can be created by calls of the form new("C1.interval", ...).

The regular usage in this package is to use the s1d.interval function.

Slots

data

a list containing data or data's name.

• score: the displayed values in the form of a vector, a factor, a name or a matching call.

• at: the index value.

• frame: a positive or null integer. It is the number of the frame containing the data (used with sys.frame(..., env = data$frame)). Only if the data are not stored (i.e. data$storeData = FALSE).

• storeData: a logical indicating if the data should be stored in the returned object. If FALSE, only the names of the data arguments are stored.

trellis.par

a list of parameters for lattice call. It will be passed directly to par.settings arguments of the lattice function.

adeg.par

a list of graphical parameters, corresponding to the ones given by adegpar() function.

lattice.call

a list to create the trellis object.

g.args

a list containing some method parameters linked with the created object of ADEg.C1 class. The specific slot for C1.density objects is:

• method: a value, bars or area, to represent either segments or areas between scores.

stats

a list of internal preliminary calculations

s.misc

a list of some others internal parameters

Call

an object of class call

Extends

Class ADEg.C1, directly.
Class ADEg, by class ADEg.C1, distance 2.
Class ADEgORtrellis, by class ADEg.C1, distance 3.
Class ADEgORADEgSORtrellis, by class ADEg.C1, distance 3.

Methods

The methods of the father classes "ADEg.C1" and "ADEg" can be used by inheritance. The specific methods for C1.interval are:

prepare

signature(object = "C1.interval"): calls the parent method (prepare for ADEg.C1) and modifies some graphical parameters used by default.

panel

signature(object = "C1.interval"): draws segments or polygons.

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot [email protected] and Stephane Dray

See Also

ADEg ADEg.C1 s1d.interval

Examples

showClass("C1.interval")

Description

Take a sequence of ADEg, ADEgS or trellis arguments and combine by columns or rows, respectively.

Usage

cbindADEg(g1, g2, ..., plot = FALSE)
rbindADEg(g1, g2, ..., plot = FALSE)

Arguments

Value

an ADEgS object

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot [email protected] and Stephane Dray

See Also

ADEg ADEgS ADEgS

Examples

data(jv73, package = "ade4")
pca1 <- ade4::dudi.pca(jv73$morpho, scannf = FALSE)
g1 <- s.label(pca1$li, plabels.optim = TRUE, plot = FALSE)
g2 <- s.class(pca1$li, jv73$fac.riv, starSize = 0, ellipseSize = 0, chullSize = 1, 
  ppolygons.alpha = 0.4, col = rainbow(12), ppoints.cex = 0, plot = FALSE)
g3 <- s.corcircle(pca1$co, pbackground.box = FALSE, plot = FALSE)
g4 <- rbindADEg(cbindADEg(g1, g2), cbindADEg(superpose(g1, g2), g3), plot = TRUE)

Description

This function allows to modify the default theme existing for adegraphics objects. The created theme also affects previously created objects.

Usage

changelatticetheme(...)

Arguments

Note

The adegraphics theme removes all margins, sets a transparent background and grey regions.

A further development will be the creation of various themes for adegraphics.

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot [email protected] and Stephane Dray

See Also

trellis.par.get trellis.par.set show.settings

Examples

if(require(lattice, quietly = TRUE)) {
  show.settings()
  changelatticetheme(list(superpose.symbol = list(pch = c(21, 22, 35), cex = 1)))
  show.settings()
  show.settings()[1]
}

Description

getcall returns the call used to create the object.

Methods

signature(object = "ADEg")

returns the slot Call of the object ADEg

signature(object = "ADEgS")

returns the slot Call of the object ADEgS

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot [email protected] and Stephane Dray

Description

This function inserts a first graphic into a previously created and/or a displayed one.

Usage

insert(graphics, oldgraphics, posi = c("bottomleft", "bottomright", "topleft", 
  "topright"), ratio = 0.2, inset = 0.0, plot = TRUE, which, dispatch = FALSE)

Arguments

Value

An object of class "ADEgS".

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot [email protected] and Stephane Dray

See Also

ADEg ADEgS

Examples

data(deug, package = "ade4")
dd1 <- ade4::dudi.pca(deug$tab, scannf = FALSE, nf = 4)
g1 <- s.label(dfxy = dd1$li, labels = rownames(dd1$li), plabels = list(cex = 0.75), plot = FALSE)
g2 <- s1d.barchart(score = dd1$eig, plot = FALSE, 
  ppolygons = list(col = c(rep("black", 2), rep("grey", 2), rep("white", 5))), 
  p1d = list(horizontal = FALSE), psub = list(position = "topright", text = "Eigenvalues"), 
  pgrid = list(draw = FALSE), pbackground = list(box = TRUE), xlim = c(0.5, 9.5))
g1
g3 <- insert(g2, plot = FALSE)

mat <- g3@positions
mat[2, ] <- c(0.8, 0, 1, 0.2)
update(g3, positions = mat, plot = FALSE)
print(g3) ## square == NULL
print(g3, square = TRUE)
print(g3, square = FALSE)

g4 <- insert(g2, g1, posi = "topleft")

data(jv73, package = "ade4")
pca1 <- ade4::dudi.pca(jv73$morpho, scannf = FALSE)
g5 <- s.value(jv73$xy, pca1$li[, 1:2], porigin.include = FALSE, plot = FALSE)
g6 <- s.corcircle(pca1$co, pbackground.box = FALSE, plot = FALSE)
g7 <- insert(g6, g5, posi = c(0.3, 0.4, 0.5, 0.6))

Description

This function transforms layout's informations into a position matrix useful for ADEgS and for lattice graphics.

Usage

layout2position(mat, widths = rep(1, NCOL(mat)), heights = rep(1, NROW(mat)), ng, 
square = FALSE)

Arguments

Value

A four-columns matrix indicating the coordinates (in normalized parent coordinates npc) of the top-right and bottom-left hand corners of each displayed figure on the device.

Note

This function is strongly inspired by the layout function in graphics package.

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot [email protected] and Stephane Dray

See Also

layout

Examples

layout2position(mat = rbind(c(0, 0, 1), c(2, 2, 1)))
layout2position(mat = cbind(c(0, 0, 1), c(2, 2, 1)), widths = c(0.5, 1.5))

Description

The method panel displays all specific graphical components.

Methods

signature(object = "C1.barchart")

draws bar charts and labels

signature(object = "C1.curve")

draws points and curves

signature(object = "C1.curves")

draws multiple points and curves

signature(object = "C1.density")

draws density curves

signature(object = "C1.dotplot")

draws segments and dots

signature(object = "C1.gauss")

draws Gauss curves and level names of each curve

signature(object = "C1.hist")

draws rectangles

signature(object = "C1.interval")

draws segments or polygons

signature(object = "S1.boxplot")

draws box-and-wiskers diagrams, mean points and labels

signature(object = "S1.class")

draws labels and lines matching with score values

signature(object = "S1.distri")

draws mean points and segments with matching labels

signature(object = "S1.label")

draws labels and its links with score points

signature(object = "S1.match")

draws score points and matching segments and labels

signature(object = "S2.arrow")

draws points, arrows and labels

signature(object = "S2.class")

draws ellipses, convex hulls, stars, labels and points

signature(object = "S2.corcircle")

draws arrows, labels and axes

signature(object = "S2.density")

draws densities and external points

signature(object = "S2.distri")

draws ellipses, stars, labels and points

signature(object = "S2.image")

draws raster image

signature(object = "S2.label")

draws points and labels

signature(object = "S2.logo")

displays the logos

signature(object = "S2.match")

draws arrows and labels

signature(object = "S2.traject")

draws points, arrows and labels

signature(object = "S2.value")

draws symbols

signature(object = "T.cont")

draws mean points and regression lines

signature(object = "T.image")

draws raster image

signature(object = "T.value")

draws symbols

signature(object = "Tr.class")

draws arrows, labels and points

signature(object = "Tr.label")

draws lines, labels and points

signature(object = "Tr.match")

draws arrows, labels and points

signature(object = "Tr.traject")

draws arrows, labels and points

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot [email protected] and Stephane Dray

Description

S3 methods to display the outputs of an analysis performed with ade4

Usage

## S3 method for class 'foucart'
kplot(object, xax = 1, yax = 2, which.tab = 1:length(object$blo), pos = -1, 
  storeData = TRUE, plot = TRUE, ...)
## S3 method for class 'mcoa'
kplot(object, xax = 1, yax = 2, which.tab = 1:nrow(object$cov2), 
  option = c("points", "axis", "columns"), pos = -1, storeData = TRUE, plot = TRUE, ...)
## S3 method for class 'mfa'
kplot(object, xax = 1, yax = 2, which.tab = 1:length(object$blo), traject = FALSE, 
  permute = FALSE, pos = -1, storeData = TRUE, plot = TRUE, ...)
## S3 method for class 'mbpcaiv'
kplot(object, xax = 1, yax = 2, which.tab =
1:length(object$blo), pos = -1, storeData = TRUE, plot = TRUE, ...)
## S3 method for class 'pta'
kplot(object, xax = 1, yax = 2, which.tab = 1:nrow(object$RV), which.graph = 1:4, 
  pos = -1, storeData = TRUE, plot = TRUE, ...)
## S3 method for class 'sepan'
kplot(object, xax = 1, yax = 2, which.tab = 1:length(object$blo), permute = FALSE, 
  traject = FALSE, posieig = "bottomleft", pos = -1, storeData = TRUE, plot = TRUE, ...)
kplotsepan.coa(object, xax = 1, yax = 2, which.tab = 1:length(object$blo), 
  permute = FALSE, posieig = "bottomleft", pos = -1, storeData = TRUE, plot = TRUE, ...)
## S3 method for class 'statis'
kplot(object, xax = 1, yax = 2, which.tab = 1:length(object$tab.names), traject = FALSE, 
  arrow = TRUE, class = NULL, pos = -1, storeData = TRUE, plot = TRUE, ...)

## S3 method for class 'acm'
plot(x, xax = 1, yax = 2, pos = -1, storeData = TRUE, plot = TRUE, ...)
## S3 method for class 'betcoi'
plot(x, xax = 1, yax = 2, pos = -1, storeData = TRUE, plot = TRUE, ...)
## S3 method for class 'betdpcoa'
plot(x, xax = 1, yax = 2, pos = -1, storeData = TRUE, plot = TRUE, ...)
## S3 method for class 'betwitdpcoa'
plot(x, xax = 1, yax = 2, pos = -1, storeData = TRUE, plot = TRUE, ...)
## S3 method for class 'betrlq'
plot(x, xax = 1, yax = 2, pos = -1, storeData = TRUE, plot = TRUE, ...)
## S3 method for class 'between'
plot(x, xax = 1, yax = 2, pos = -1, storeData = TRUE, plot = TRUE, ...)
## S3 method for class 'coinertia'
plot(x, xax = 1, yax = 2, pos = -1, storeData = TRUE, plot = TRUE, ...)
## S3 method for class 'discrimin'
plot(x, xax = 1, yax = 2, pos = -1, storeData = TRUE, plot = TRUE, ...)
## S3 method for class 'dpcoa'
plot(x, xax = 1, yax = 2, pos = -1, storeData = TRUE, plot = TRUE, ...)
## S3 method for class 'fca'
plot(x, xax = 1, yax = 2, pos = -1, storeData = TRUE, plot = TRUE, ...)
## S3 method for class 'foucart'
plot(x, xax = 1, yax = 2, pos = -1, storeData = TRUE,
plot = TRUE, ...)
## S3 method for class 'krandboot'
plot(x, pos = -1, storeData = TRUE, plot = TRUE, ...)
## S3 method for class 'krandxval'
plot(x, pos = -1, storeData = TRUE, plot = TRUE, ...)
## S3 method for class 'mcoa'
plot(x, xax = 1, yax = 2, pos = -1, storeData = TRUE, plot = TRUE, ...)
## S3 method for class 'mfa'
plot(x, xax = 1, yax = 2, pos = -1, storeData = TRUE,
plot = TRUE, ...)
## S3 method for class 'multiblock'
plot(x, xax = 1, yax = 2, pos = -1, storeData = TRUE, plot = TRUE, ...)
## S3 method for class 'multispati'
plot(x, xax = 1, yax = 2, pos = -1, storeData = TRUE, plot = TRUE, ...)
## S3 method for class 'niche'
plot(x, xax = 1, yax = 2, pos = -1, storeData = TRUE, plot = TRUE, ...)
## S3 method for class 'pcaiv'
plot(x, xax = 1, yax = 2, pos = -1, storeData = TRUE, plot = TRUE, ...)
## S3 method for class 'pta'
plot(x, xax = 1, yax = 2, pos = -1, storeData = TRUE, plot = TRUE, ...)
## S3 method for class 'procuste'
plot(x, xax = 1, yax = 2, pos = -1, storeData =
TRUE, plot = TRUE, ...)
## S3 method for class 'randboot'
plot(x, pos = -1, storeData = TRUE, plot = TRUE, ...)
## S3 method for class 'randxval'
plot(x, pos = -1, storeData = TRUE, plot = TRUE, ...)
## S3 method for class 'rlq'
plot(x, xax = 1, yax = 2, pos = -1, storeData = TRUE, plot = TRUE, ...)
## S3 method for class 'sepan'
plot(x, pos = -1, storeData = TRUE, plot = TRUE, ...)
## S3 method for class 'statis'
plot(x, xax = 1, yax = 2, pos = -1, storeData = TRUE, plot = TRUE, ...)
## S3 method for class 'witcoi'
plot(x, xax = 1, yax = 2, pos = -1, storeData = TRUE, plot = TRUE, ...)
## S3 method for class 'witdpcoa'
plot(x, xax = 1, yax = 2, pos = -1, storeData = TRUE, plot = TRUE, ...)
## S3 method for class 'within'
plot(x, xax = 1, yax = 2, pos = -1, storeData = TRUE, plot = TRUE, ...)
## S3 method for class 'witrlq'
plot(x, xax = 1, yax = 2, pos = -1, storeData = TRUE, plot = TRUE, ...)
## S3 method for class 'bcaloocv'
plot(x, xax = 1, yax = 2, pos = -1, storeData = TRUE, plot = TRUE, ...)
## S3 method for class 'discloocv'
plot(x, xax = 1, yax = 2, pos = -1, storeData = TRUE, plot = TRUE, ...)

## S3 method for class 'dudi'
scatter(x, xax = 1, yax = 2, permute = FALSE, posieig = "topleft", prop = FALSE, 
  density.plot = ifelse(permute, ncol(x$tab) > 1000, nrow(x$tab) > 1000), plot = TRUE, 
  storeData = TRUE, pos = -1, ...)
## S3 method for class 'coa'
scatter(x, xax = 1, yax = 2, method = 1:3, posieig = "topleft", pos = -1, 
  storeData = TRUE, plot = TRUE, ...)
## S3 method for class 'pco'
scatter(x, xax = 1, yax = 2, posieig = "topleft", pos = -1, storeData = TRUE, 
  plot = TRUE, ...)
## S3 method for class 'nipals'
scatter(x, xax = 1, yax = 2, posieig = "topleft", pos = -1, storeData = TRUE, 
  plot = TRUE, ...)

## S3 method for class 'acm'
score(x, xax = 1, which.var = NULL, type = c("points", "boxplot"), pos = -1, 
  storeData = TRUE, plot = TRUE, ...)
## S3 method for class 'mix'
score(x, xax = 1, which.var = NULL, type = c("points", "boxplot"), pos = -1, 
  storeData = TRUE, plot = TRUE, ...)

## S3 method for class 'pca'
score(x, xax = 1, which.var = NULL, pos = -1, storeData = TRUE, plot = TRUE, ...)

## S3 method for class 'dudi'
screeplot(x, col.kept = "grey", col = "white", pos = -1, plot = TRUE, ...)

## S3 method for class 'dudi'
biplot(x, pos = -1, plot = TRUE, ...)

Arguments