Plot the graphs for a Principal Component Analysis (PCA) with supplementary individuals, supplementary quantitative variables and supplementary categorical variables.

```
# S3 method for PCA
plot(x, axes = c(1, 2), choix = c("ind","var","varcor"),
ellipse = NULL, xlim = NULL, ylim = NULL, habillage="none",
col.hab = NULL, col.ind="black", col.ind.sup="blue",
col.quali="magenta", col.quanti.sup="blue", col.var="black",
label = c("all","none","ind","ind.sup","quali","var","quanti.sup"),
invisible = c("none","ind","ind.sup","quali","var","quanti.sup"),
lim.cos2.var = 0., 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, …)
```

x

an object of class PCA

axes

a length 2 vector specifying the components to plot

choix

the graph to plot ("ind" for the individuals, "var" for the variables, "varcor" for a graph with the correlation circle when `scale.unit=FALSE`

)

ellipse

boolean (NULL by default), if not null, draw ellipses around the individuals, and use the results of `coord.ellipse`

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'

habillage

give no color for the individuals ("none"), a color for each individual ("ind"), or color the individuals among a categorical variable (give the number of the categorical variable)

col.hab

a vector with the color to use for the individuals

col.ind

a color for the individuals only if there is not habillage

col.ind.sup

a color for the supplementary individuals only if there is not habillage

col.quali

a color for the categories of categorical variables only if there is not habillage

col.quanti.sup

a color for the quantitative supplementary variables

col.var

a color for the variables

label

a list of character for the elements which are labelled (by default, all the elements are labelled ("ind", ind.sup", "quali", "var", "quanti.sup"))

invisible

string indicating if some points should not be drawn ("ind", "ind.sup" or "quali" for the individual graph and "var" or "quanti.sup" for the correlation circle graph)

lim.cos2.var

value of the square cosinus under the variables are not drawn

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; only used when `graph.type="classic"`

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); only used when `graph.type="classic"`

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, ...

Returns the individuals factor map and the variables factor map.

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 variables) 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.

`ggoptions`

is a list that gives some ggplot2 options when the graph.type="ggplot" is used. Use for instance ggoptions(list(size=3,title.size=10,bg.color="orange")) if you want to modify the size of the points and labels, the title size and the background color.
Below you can see the options and the default values:
size = 4, #label size (point size = size/3)
point.shape = 19, #points shape
line.lty = 2, #origin linetypes (0="blank", 1="solid", 2="dashed", 3="dotted",...)
line.lwd = 0, #origin lines width
line.color = "black", #origin lines color
segment.lty = 1, #arrow linetypes (0="blank", 1="solid", 2="dashed", 3="dotted",...)
segment.lwd = 0, #arrow width
circle.lty = 1, #circle linetypes (0="blank", 1="solid", 2="dashed", 3="dotted",...)
circle.lwd = 0, #circle width
circle.color = "black", #circle color
low.col.quanti = "blue", #for quantitative variables, low color to be used
high.col.quanti = "red3", #for quantitative variables, high color to be used

# NOT RUN { data(decathlon) res.pca <- PCA(decathlon, quanti.sup = 11:12, quali.sup = 13) plot(res.pca, habillage = 13, cex=0.8) # } # NOT RUN { plot(res.pca, habillage = "cos2") plot(res.pca, habillage = "100m") plot(res.pca, habillage = c("Competition","100m")) # } # NOT RUN { ## To automatically draw ellipses around the barycentres of the categorical variables plotellipses(res.pca) ## Selection of some individuals plot(res.pca,select="contrib 7") # plot the 7 individuals with the highest contribution plot(res.pca,select="cos2 0.8") # plot the individuals with cos2 greater than 0.8 plot(res.pca,select="cos2 5") # plot the 5 individuals with the highest cos2 plot(res.pca,choix="var",select="cos2 0.6") # plot the variables with cos2 greater than 0.6 plot(res.pca,habillage="100m", ggoptions=list(low.col.quanti="grey90",high.col.quanti="grey10"),legend=list(x="bottom")) ## You can modify the ggplot graphs as ususal with ggplot2 require(ggplot2) gr <- plot(res.pca) gr + theme(panel.grid.major = element_blank(), plot.title=element_text(size=14, color="blue"), axis.title = element_text(size=12, color="red")) ## To draw classical R graphs plot(res.pca, graph.type = "classic") # }

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