viz_variables: Visualize Variables Factor Map

Description

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,
  extra_quali = NULL,
  extra_quanti = NULL,
  color = NULL,
  fill = FALSE,
  symbol = FALSE,
  size = c(1, 6),
  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),
  color = FALSE,
  fill = FALSE,
  symbol = FALSE,
  legend = NULL
)
# S4 method for PCA
viz_variables(
  x,
  ...,
  axes = c(1, 2),
  active = TRUE,
  sup = TRUE,
  labels = list(filter = "contribution", n = 10),
  extra_quali = NULL,
  extra_quanti = NULL,
  color = NULL,
  symbol = NULL,
  size = 1,
  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,
  extra_quali = NULL,
  extra_quanti = NULL,
  color = NULL,
  fill = FALSE,
  symbol = FALSE,
  size = c(1, 6),
  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),
  color = FALSE,
  fill = FALSE,
  symbol = FALSE,
  legend = NULL
)

Value

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

Arguments

x: A CA, MCA or PCA object.
...: Further graphical parameters.
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, filter (a string specifying how to filter the labels to be drawn) and n (an integer specifying the number of labels to be drawn). See examples below.
extra_quali: An optional vector of qualitative data for aesthetics mapping.
extra_quanti: An optional vector of quantitative data for aesthetics mapping. If a single character string is passed, it must be one of "observation", "mass", "sum", "contribution" or "cos2" (see augment()).
color: The colors for lines and points (will be mapped to extra_quanti or extra_quali; if both are set, the latter has priority). Ignored if set to FALSE. If NULL, the default color scheme will be used.
fill: The background colors for points (will be mapped to extra_quanti or extra_quali; if both are set, the latter has priority). Ignored if set to FALSE.
symbol: A vector of plotting characters or symbols (will be mapped to extra_quali). This can either be a single character or an integer code for one of a set of graphics symbols. If symbol is a named a named vector, then the symbols will be associated with their name within extra_quali. Ignored if set to FALSE.
size: A length-two numeric vector giving range of possible sizes (greater than 0; will be mapped to extra_quanti). Ignored if set to FALSE.
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.

Author

N. Frerebeau

Examples

Run this code

## Load data
data("iris")

## Compute principal components analysis
X <- pca(iris, scale = TRUE, sup_quali = "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, extra_quanti = iris$Petal.Length, symbol = 16, size = c(1, 2))
viz_individuals(X, extra_quanti = iris$Petal.Length, symbol = 16, size = c(1, 2),
                color = grDevices::hcl.colors(12, "RdPu"))

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

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

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

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