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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,
  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,
  top = 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,
  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

A CA, MCA or PCA object.

...

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?

highlight

A vector specifying the information to be highlighted. If NULL (the default), no highlighting is applied. If a single character string is passed, it must be one of "observation", "mass", "sum", "contribution" or "cos2" (see augment()). Any unambiguous substring can be given.

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 to graphics::legend(); names of the list are used as argument names. If NULL, no legend is displayed.

top

An integer specifying the number of labels to draw. Only the labels of the top \(n\) observations contributing the most to the factorial map will be drawn. If NULL, all labels are drawn. Only used if labels is TRUE.

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.

Note

Be careful: graphical parameters are silently recycled.

See also

Author

N. Frerebeau

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))