plot.MFA: Draw the Multiple Factor Analysis (MFA) graphs

In FactoMineR: Multivariate Exploratory Data Analysis and Data Mining

Draw the Multiple Factor Analysis (MFA) graphs

Description

Draw the Multiple Factor Analysis (MFA) graphs.

Usage

## S3 method for class 'MFA'
plot(x, axes = c(1, 2), choix = c("ind","var","group","axes","freq"), 
    ellipse=NULL, ellipse.par=NULL,
    lab.grpe=TRUE, lab.var=TRUE, lab.ind=TRUE, 
    lab.par=FALSE, lab.col=TRUE, ncp=2, habillage="group", col.hab=NULL, 
    invisible = c("none","ind","ind.sup","quanti","quanti.sup",
	"quali","quali.sup","row","row.sup","col","col.sup"), 
	partial = NULL, lim.cos2.var = 0., 
    chrono = FALSE, xlim = NULL, ylim = NULL, 
    title = NULL, palette = NULL, 
	autoLab = c("auto","yes","no"), new.plot = FALSE, 
	select = NULL, unselect = 0.7, shadowtext = FALSE, 
	legend = list(bty = "y", x = "topleft"),
	graph.type = c("ggplot","classic"), ggoptions = NULL, ...)

Arguments

x	an object of class MFA
choix	a string corresponding to the graph that you want to do ("ind" for the individual or categorical variables graph, "var" for the quantitative variables graph, "freq" for the frequence or contingency tables, "axes" for the graph of the partial axes, "group" for the groups representation)
axes	a length 2 vector specifying the components to plot
ellipse	boolean (NULL by default), if not null, draw ellipses around the individuals, and use the results of coord.ellipse
ellipse.par	boolean (NULL by default), if not null, draw ellipses around the partial individuals, and use the results of coord.ellipse
lab.grpe	boolean, if TRUE, the labels of the groups are drawn
lab.var	boolean, if TRUE, the labels of the variables are drawn
lab.ind	boolean, if TRUE, the labels of the mean points are drawn
lab.par	boolean, if TRUE, the labels of the partial points are drawn
lab.col	boolean, if TRUE, the labels of the columns for the contingency tables are drawn
ncp	number of principal components drawn for the separate analyses for the graph of the partial axes
habillage	string corresponding to the color which are used. If "ind", one color is used for each individual; if "group" the individuals are colored according to the group; else if it is the name or the position of a categorical variable, it colors according to the different categories of this variable
col.hab	the colors to use. By default, colors are chosen
invisible	list of string; for choix ="ind", the individuals can be omit (invisible = "ind"), or supplementary individuals (invisible="ind.sup") or the center of gravity of the categorical variables (invisible= "quali" or "quali.sup" for the supplementary categories); if invisible = c("ind","ind.sup"), just the centers of gravity are drawn; if choix="var", invisible="quanti" suppress the active variable and invisible = "quanti.sup" suppress the supplementary variables
partial	list of the individuals or of the center of gravity for which the partial points should be drawn (by default, partial = NULL and no partial points are drawn)
lim.cos2.var	value of the square cosinus under with the points are not drawn
chrono	boolean, if TRUE, the partial points of a same point are linked (useful when groups correspond to different moment)
xlim	range for the plotted 'x' values, defaulting to the range of the finite values of 'x'
ylim	range for the plotted 'y' values, defaulting to the range of the finite values of 'y'
title	string corresponding to the title of the graph you draw (by default NULL and a title is chosen)
palette	the color palette used to draw the points. By default colors are chosen. If you want to define the colors : palette=palette(c("black","red","blue")); or you can use: palette=palette(rainbow(30)), or in black and white for example: palette=palette(gray(seq(0,.9,len=25)))
autoLab	if autoLab="auto", autoLab is equal to "yes" if there are less than 50 elements and "no" otherwise; if "yes", the labels of the drawn elements are placed in a "good" way (can be time-consuming if many elements), and if "no" the elements are placed quickly but may overlap
new.plot	boolean, if TRUE, a new graphical device is created
select	a selection of the elements that are drawn; see the details section
unselect	may be either a value between 0 and 1 that gives the transparency of the unselected objects (if unselect=1 the transparceny is total and the elements are not drawn, if unselect=0 the elements are drawn as usual but without any label) or may be a color (for example unselect="grey60")
shadowtext	boolean; if true put a shadow on the labels (rectangles are written under the labels which may lead to difficulties to modify the graph with another program)
legend	a list of arguments that defines the legend if needed (when individuals are drawn according to a variable); see the arguments of the function legend
graph.type	a character that gives the type of graph used: "ggplot" or "classic"
ggoptions	a list that gives the graph options when grah.type="ggplot" is used. See the optines and the default values in the details section
...	further arguments passed to or from other methods, such as cex, cex.main, ...

Details

The argument autoLab = "yes" is time-consuming if there are many labels that overlap. In this case, you can modify the size of the characters in order to have less overlapping, using for example cex=0.7.
The select argument can be used in order to select a part of the elements (individuals if you draw the graph of individuals, or variables if you draw the graph of variabless) that are drawn. For example, you can use:
select = 1:5 and then the elements 1:5 are drawn.
select = c("name1","name5") and then the elements that have the names name1 and name5 are drawn.
select = "coord 10" and then the 10 elements (individuals, variables, frequencies) that have the highest (squared) coordinates on the 2 chosen dimensions are drawn.
select = "contrib 10" and then the 10 elements (individuals, variables, frequencies) that have the highest contribution on the 2 dimensions of your plot are drawn.
select = "cos2 5" and then the 5 elements (individuals, variables, frequencies) that have the highest cos2 on the 2 dimensions of your plot are drawn.
selectMod = "contrib 5", the 5 categories that contribute the most to the two dimensions are drawn.
selectMod = "cos2 0.5", the categories that have a cos2 greater than 0.5 on the two dimensions are drawn.
selectMod = "v.test 2", the categories that have a v.test higher than the value on one of the two dimensions are drawn.

Value

Returns the individuals factor map and the variables factor map.

Author(s)

Francois Husson [e-mail], Jeremy Mazet

See Also

MFA

Examples

## Not run: 
data(wine)
res <- MFA(wine,group=c(2,5,3,10,9,2),type=c("n",rep("s",5)),ncp=5,
    name.group=c("orig","olf","vis","olfag","gust","ens"),
    num.group.sup=c(1,6),graph=FALSE)
plot(res, choix = "ind")
plot(res, choix = "ind", partial="all")
plot(res, choix = "ind", habillage="Label")
plot(res, choix = "var", habillage="group")
plot(res, choix = "axes")

data(wine)
res <- MFA(wine, group=c(2,5,3,10,9,2), type=c("n",rep("s",5)),
    ncp=5, name.group=c("orig","olf","vis","olfag","gust","ens"),
    num.group.sup=c(1,6))
summary(res)
barplot(res$eig[,1],main="Eigenvalues",names.arg=1:nrow(res$eig))

#### Confidence ellipses around categories per variable
plotellipses(res)
plotellipses(res,keepvar="Label") ## for 1 variable

#### Interactive graph
liste = plotMFApartial(res)
plot(res,choix="ind",habillage = "Terroir")

###Example with groups of categorical variables
data (poison)
MFA(poison, group=c(2,2,5,6), type=c("s","n","n","n"),
    name.group=c("desc","desc2","symptom","eat"),
    num.group.sup=1:2)

###Example with groups of frequency tables
data(mortality)
res<-MFA(mortality,group=c(9,9),type=c("f","f"),
    name.group=c("1979","2006"))

## End(Not run)

FactoMineR documentation built on May 29, 2024, 3:36 a.m.