Visualize Individuals Factor Map

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,
  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 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,
  labels_max = 10,
  highlight = NULL,
  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?
labels_max: An integer specifying the number of labels to draw. Only the labels of the \(n\) observations with highest \(cos^2\) values will be drawn. If NULL, all labels are drawn. Only used if labels is TRUE.
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()).
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.

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.
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.

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))