Methods to display the outputs of an analysis performed with ade4

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Description

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

Usage

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## 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 '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, 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

object, x

objects used to select a method

xax

an integer (or a vector) indicating which column(s) of object or x is(are) plotted on the x-axis

yax

an integer (or a vector) indicating which column(s) of object or x is(are) plotted on the y-axis

which.tab

a numeric vector (used in kplot.*) containing the numbers of the tables used for the analysis

option

a string of characters (only used in kplot.mfa) indicating the drawing option: points plot of the projected scattergram onto the co-inertia axes, axis projections of inertia axes onto the co-inertia axes, columns projections of variables onto the synthetic variables planes.

which.graph

an integer between 1 and 4 (only used in kplot.pta) indicating the drawing option. For each table of which.tab, are drawn: 1 the projections of the principal axes, 2 the projections of the rows, 3 the projections of the columns, 4 the projections of the principal components onto the planes of the compromise.

permute

a logical value (used in kplot.sepan, kplotsepan.coa and scatter.dudi). If FALSE, the rows are plotted by points or density surface and the columns by arrows. If TRUE, it is the opposite.

traject

a logical value (used in kplot.sepan and kplot.statis) indicating whether the trajectories between rows should be drawn in a natural order

posieig

a character value or a two-length numeric vector (in normalized parent coordinates npc from 0 to 1) or none value indicating the position of the eigenvalues bar plot (used in kplot.sepan, kplotsepan.coa and scatter.*).

arrow

a logical value (only used in kplot.statis) indicating whether the column factorial diagrams should be plotted

class

if not NULL, a factor of length equal to the number of the total columns of the K-tables (only used in kplot.statis)

prop

a logical value (only used in scatter.dudi) indicating if the size of the arrows' labels is proportional to the analysis score.

density.plot

a logical value (only used in scatter.dudi)indicating if the points are displayed as density surface (using s.density).

method

an integer between 1 and 3 (only used in scatter.coa) indicating the drawing option. Are drawn: 1 rows and columns with the coordinates of lambda variance, 2 rows variance 1 and columns by averaging, 3 columns variance 1 and rows by averaging.

which.var

the numbers of the kept columns for the analysis, otherwise all columns (used in score.*)

type

a string of characters (only used in score.acm) indicating if points (points) or boxplot (boxplot) are used to represent levels of factors

col.kept

one color value to color the kept axes in the barchart (used in screeplot.dudi)

col

one color value to color the axes in the barchart (used in screeplot.dudi)

plot

a logical indicating if the graphics is displayed

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

pos

an integer indicating the position of the environment where the data are stored, relative to the environment where the function is called. Useful only if storeData is FALSE

...

additional graphical parameters (see adegpar and trellis.par.get)

Value

Returns an ADEg or an ADEgS object. The result is displayed if plot is TRUE.

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Stephane Dray

References

See ade4 website: <URL: http://pbil.univ-lyon1.fr/ADE-4/>

Examples

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cat("To run the example on 'topic'\n")
cat("Type in your R console: example(topic, package = 'ade4') \n")

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