Draw the Multiple Correspondence Analysis (MCA) graphs.
# S3 method for MCA
plot(x, axes = c(1, 2), choix=c("ind","var","quanti.sup"),
xlim = NULL, ylim = NULL,
invisible = c("none","ind","var","ind.sup","quali.sup","quanti.sup"),
col.ind = "black", col.var = "red", col.quali.sup = "darkgreen",
col.ind.sup = "blue", col.quanti.sup = "blue",
label = c("all","none","ind","var","ind.sup","quali.sup","quanti.sup"),
title = NULL, habillage = "none",
palette = NULL, autoLab = c("auto","yes","no"), new.plot = FALSE,
select = NULL, selectMod = NULL, unselect = 0.7,
shadowtext = FALSE, legend = list(bty = "y", x = "topleft"),
graph.type = c("ggplot","classic"), ggoptions = NULL, ...)Returns the individuals factor map and the variables factor map.
an object of class MCA
a length 2 vector specifying the components to plot
the graph to plot ("ind" for the individuals and the categories, "var" for the variables, "quanti.sup" for the supplementary quantitative variables)
range for the plotted 'x' values, defaulting to the range of the finite values of 'x'
range for the plotted 'y' values, defaulting to the range of the finite values of 'y'
string indicating if some points should not be drawn ("ind", "var", "ind.sup", "quali.sup", "quanti.sup")
a color for the individuals, if color ="none" the label is not written
a color for the categories of categorical variables, if color ="none" the label is not written
a color for the categorical supplementary variables, if color ="none" the label is not written
a color for the supplementary individuals only if there is not habillage, if color ="none" the label is not written
a color for the supplementary quantitative variables, if color ="none" the label is not written
print the labels of the points; "all" print all the labels; may be a vector with "ind" (for the individuals),"ind.sup" (for the supplementary individuals),"var" (for the active categories), "quali.sup" "var" (for the supplementary categories)
string corresponding to the title of the graph you draw (by default NULL and a title is chosen)
string corresponding to the color which are used. If "none", one color is used for the individual, another one for the categorical variables; if "quali", one color is used for each categorical variables; else if it is the position of a categorical variable, it colors according to the different categories of this variable
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)))
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
boolean, if TRUE, a new graphical device is created
a selection of the elements that are drawn; see the details section
a selection of the categories that are drawn; see the details section
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")
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)
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
a character that gives the type of graph used: "ggplot" or "classic"
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, ...
Francois Husson francois.husson@institut-agro.fr
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 that have the highest (squared) coordinates on the 2 chosen dimensions are drawn.
select = "contrib 10" and then the 10 elements that have the highest contribution on the 2 dimensions of your plot are drawn.
select = "cos2 5" and then the 5 elements that have the highest cos2 on the 2 dimensions of your plot are drawn.
select = "dist 8" and then the 8 elements that have the highest distance to the center of gravity are drawn.
The selectMod argument can be used in order to select the categories that are drawn.
MCA
data (poison)
res.mca = MCA (poison, quali.sup = 3:4, quanti.sup = 1:2, graph=FALSE)
plot(res.mca,invisible=c("var","quali.sup"))
plot(res.mca,invisible="ind")
plot(res.mca,choix="var")
plot(res.mca,invisible=c("ind"), selectMod="cos2 10")
if (FALSE) {
plot(res.mca, selectMod="cos2 5", select="cos2 5")
## You can modify the ggplot graphs as ususal with ggplot2
require(ggplot2)
gr <- plot(res.mca)
gr + theme(panel.grid.major = element_blank(),
plot.title=element_text(size=14, color="blue"),
axis.title = element_text(size=12, color="red"))
}
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