Plots column/variable principal coordinates.
Usage
viz_variables(x, ...)
viz_columns(x, ...)
# S4 method for MultivariateAnalysis
viz_columns(
x,
...,
axes = c(1, 2),
active = TRUE,
sup = TRUE,
labels = FALSE,
labels_max = 10,
highlight = NULL,
xlim = NULL,
ylim = NULL,
main = NULL,
sub = NULL,
panel.first = NULL,
panel.last = NULL,
legend = list(x = "topleft")
)
# S4 method for MultivariateBootstrap
viz_columns(x, ..., axes = c(1, 2))
# S4 method for PCA
viz_variables(
x,
...,
axes = c(1, 2),
active = TRUE,
sup = TRUE,
labels = TRUE,
labels_max = 10,
highlight = NULL,
xlim = NULL,
ylim = NULL,
main = NULL,
sub = NULL,
panel.first = NULL,
panel.last = NULL,
legend = list(x = "topleft")
)
# S4 method for CA
viz_variables(
x,
...,
axes = c(1, 2),
active = TRUE,
sup = TRUE,
labels = FALSE,
labels_max = 10,
highlight = NULL,
xlim = NULL,
ylim = NULL,
main = NULL,
sub = NULL,
panel.first = NULL,
panel.last = NULL,
legend = list(x = "topleft")
)
# S4 method for BootstrapPCA
viz_variables(x, ..., axes = c(1, 2))
Arguments
- x
- ...
Further graphical parameters (see details).
- axes
A length-two
numeric
vector giving the dimensions to be plotted.- active
A
logical
scalar: should the active observations be plotted?- sup
A
logical
scalar: should the supplementary observations be plotted?- labels
A
logical
scalar: should labels be drawn?- labels_max
An
integer
specifying the number of labels to draw. Only the labels of the \(n\) variables contributing the most to the factorial map will be drawn. IfNULL
, all labels are drawn. Only used iflabels
isTRUE
.- highlight
A vector specifying the information to be highlighted. If
NULL
(the default), no highlighting is applied. If a singlecharacter
string is passed, it must be the name of a categorical variable, or one of "observation
", "mass
", "sum
", "contribution
" or "cos2
" (seeaugment()
).- xlim
A length-two
numeric
vector giving the x limits of the plot. The default value,NULL
, indicates that the range of the finite values to be plotted should be used.- ylim
A length-two
numeric
vector giving the y limits of the plot. The default value,NULL
, indicates that the range of the finite values to be plotted should be used.- main
A
character
string giving a main title for the plot.- sub
A
character
string giving a subtitle for the plot.- panel.first
An
expression
to be evaluated after the plot axes are set up but before any plotting takes place. This can be useful for drawing background grids.- panel.last
An
expression
to be evaluated after plotting has taken place but before the axes, title and box are added.- legend
A
list
of additional arguments to be passed tographics::legend()
; names of the list are used as argument names. IfNULL
, no legend is displayed.
Value
viz_*()
is called for its side-effects: it results in a graphic
being displayed. Invisibly returns x
.
Details
Commonly used graphical parameters are:
pch
A vector of plotting characters or symbols. This can either be a single character or an integer code for one of a set of graphics symbols.
cex
A numerical vector giving the amount by which plotting characters and symbols should be scaled relative to the default.
lty
A vector of line types.
lwd
A vector of line widths.
col
The colors for lines and points. Multiple colors can be specified so that each point can be given its own color.
bg
The background color for the open plot symbols given by
pch = 21:25
.
See also
Other plot methods:
biplot()
,
screeplot()
,
viz_contributions()
,
viz_individuals()
,
viz_wrap
,
wrap
Examples
## Load data
data("iris")
## Compute principal components analysis
X <- pca(iris, scale = TRUE)
#> 1 qualitative variable was removed: Species.
## Plot individuals
viz_individuals(X, panel.last = graphics::grid())
## Plot variables
viz_variables(X, panel.last = graphics::grid())
## Graphical parameters
## Continuous values
viz_individuals(X, highlight = iris$Petal.Length, pch = 16)
viz_individuals(X, highlight = iris$Petal.Length, pch = 16,
col = grDevices::hcl.colors(12, "RdPu"))
viz_individuals(X, highlight = iris$Petal.Length, pch = 16,
col = grDevices::hcl.colors(12, "RdPu"),
cex = c(1, 2))
viz_variables(X, highlight = "contribution",
col = grDevices::hcl.colors(12, "BluGrn", rev = TRUE),
lwd = c(1, 5))
## Discrete values
viz_individuals(X, highlight = iris$Species, pch = 21:23)
viz_individuals(X, highlight = iris$Species, pch = 21:23,
bg = c("#004488", "#DDAA33", "#BB5566"),
col = "black")
viz_variables(X, highlight = c("Petal", "Petal", "Sepal", "Sepal"),
col = c("#EE7733", "#0077BB"),
lty = c(1, 3))