Draw the Correspondence Analysis (CA) graphs.
# S3 method for CA
plot(x, axes = c(1, 2),
xlim = NULL, ylim = NULL,
invisible = c("none","row","col","row.sup","col.sup","quali.sup"),
choix = c("CA","quanti.sup"), col.row="blue", col.col="red",
col.row.sup="darkblue", col.col.sup="darkred",
col.quali.sup="magenta", col.quanti.sup="blue",
label = c("all","none","row","row.sup","col","col.sup","quali.sup"),
title = NULL, palette = NULL, autoLab = c("auto","yes","no"),
new.plot=FALSE, selectRow = NULL, selectCol = NULL,
unselect = 0.7, shadowtext = FALSE, habillage = "none",
legend = list(bty = "y", x = "topleft"),
graph.type = c("ggplot","classic"), ggoptions = NULL, ...)Returns the factor map with the joint plot of CA.
an object of class CA
a length 2 vector specifying the components to plot
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 be unlabelled ("row", "col", "row.sup", "col.sup","quali.sup")
the graph to plot ("CA" for the CA map, "quanti.sup" for the supplementary quantitative variables)
a color for the rows points
a color for columns points
a color for the supplementary rows points
a color for supplementary columns points
a color for the supplementary categorical variables
a color for the supplementary quantitative variables
a list of character for the elements which are labelled (by default, all the elements are labelled ("row", "row.sup", "col", "col.sup","quali.sup")
string corresponding to the title of the graph you draw (by default NULL and a title is chosen)
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 rows that are drawn; see the details section
a selection of the columns 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)
color the individuals among a categorical variable (give the number of the categorical supplementary variable or its name)
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 selectRow and selectCol arguments can be used in order to select a part of the elements that are drawn.
For example, you can use:
selectRow = 1:5 and then the rows 1 to 5 are drawn.
select = c("name1","name5") and then the rows that have the names name1 and name5 are drawn.
select = "coord 10" and then the 10 rows (10 active and 10 supplementaries) that have the highest (squared) coordinates on the 2 chosen dimensions are drawn.
select = "contrib 10" and then the 10 rows (10 active) that have the highest contribution on the 2 dimensions of your plot are drawn.
select = "cos2 5" and then the 5 rows (5 actives and 5 supplementaries) that have the highest cos2 on the 2 dimensions of your plot are drawn.
select = "dist 8" and then the 8 rows (8 actives and 8 supplementaries) that have the highest distance to the center of gravity are drawn.
CA
data(children)
res.ca <- CA (children, col.sup = 6:8, row.sup = 15:18)
## select rows and columns that have a cos2 greater than 0.8
plot(res.ca, selectCol="cos2 0.8", selectRow="cos2 0.8")
if (FALSE) {
## You can modify the ggplot graphs as ususal with ggplot2
require(ggplot2)
gr <- plot(res.ca)
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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