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Plots row/individual principal coordinates.

Usage

viz_individuals(x, ...)

viz_rows(x, ...)

# S4 method for MultivariateAnalysis
viz_rows(
  x,
  ...,
  axes = c(1, 2),
  active = TRUE,
  sup = TRUE,
  labels = FALSE,
  highlight = NULL,
  color = NULL,
  symbol = 16,
  size = c(1, 3),
  xlim = NULL,
  ylim = NULL,
  main = NULL,
  sub = NULL,
  panel.first = NULL,
  panel.last = NULL,
  legend = list(x = "topleft")
)

# S4 method for BootstrapCA
viz_rows(x, ..., axes = c(1, 2))

# S4 method for PCA
viz_individuals(
  x,
  ...,
  axes = c(1, 2),
  active = TRUE,
  sup = TRUE,
  labels = FALSE,
  highlight = NULL,
  color = NULL,
  symbol = 16,
  size = c(1, 3),
  xlim = NULL,
  ylim = NULL,
  main = NULL,
  sub = NULL,
  panel.first = NULL,
  panel.last = NULL,
  legend = list(x = "topleft")
)

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? Labeling a large number of points can be computationally expensive and make the graph difficult to read. A selection of points to label can be provided using a list of two named elements, how (a string specifying how to select the labels to be drawn) and n (an integer specifying the number of labels to be drawx). See examples below.

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 the name of a categorical variable, or one of "observation", "mass", "sum", "contribution" or "cos2" (see augment()).

color

The colors for lines and points (will be mapped to highlight).

symbol

A vector of plotting characters or symbols.

size

A length-two numeric vector giving range of possible sizes (greater than 0; (will be mapped to highlight).

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.

Value

viz_*() is called for its side-effects: it results in a graphic being displayed. Invisibly returns x.

Note

Be careful: graphical parameters are silently recycled.

See also

Other plot methods: biplot(), screeplot(), viz_contributions(), viz_variables(), viz_wrap, wrap

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())


## Labels of the 10 individuals with highest cos2
viz_individuals(X, labels = list(how = "cos2", n = 10))


## Plot variables
viz_variables(X, panel.last = graphics::grid())


## Graphical parameters
## Continuous values
viz_individuals(X, highlight = iris$Petal.Length, symbol = 16, size = c(1, 2))

viz_individuals(X, highlight = iris$Petal.Length, symbol = 16, size = c(1, 2),
                color = grDevices::hcl.colors(12, "RdPu"))


viz_variables(X, highlight = "contribution",
              color = grDevices::hcl.colors(12, "BluGrn", rev = TRUE),
              size = c(0, 1))


## Discrete values
viz_individuals(X, highlight = iris$Species, symbol = 21:23)

viz_individuals(X, highlight = iris$Species, symbol = 21:23,
                fill = c("#004488", "#DDAA33", "#BB5566"),
                color = "black")


viz_variables(X, highlight = c("Petal", "Petal", "Sepal", "Sepal"),
              color = c("#EE7733", "#0077BB"),
              symbol = c(1, 3))