Description Usage Arguments Details Value Author(s) See Also Examples

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

1 2 3 4 5 6 7 8 9 10 11 12 | ```
## S3 method for class '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 |

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

`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 |

`new.plot` |
boolean, if TRUE, a new graphical device is created; only used when |

`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 |

`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 |

`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 |

`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, ... |

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

Returns the individuals factor map and the variables factor map.

Francois Husson husson@agrocampus-ouest.fr

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 | ```
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"))
## End(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")
``` |

```
Loading required package: ggplot2
```

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