pca.biplot: pca.biplot

In StefaanVerwimp/Biplot: A customizable correlational biplot function

Description

A customizable correlational biplot function. PC's are scaled to unit variance.

Usage

pca.biplot(
  data,
  center = TRUE,
  scale = FALSE,
  pcx = 1,
  pcy = 2,
  groups = 1,
  col = NULL,
  pch = 1,
  ellipse = FALSE,
  ellipse.alpha = 0.2,
  ellipse.conf = 0.68,
  ellipse.lwd = 2,
  arrow.options,
  label.options,
  abbrev = FALSE,
  circle = TRUE,
  circle.options,
  legend = TRUE,
  legend.pos = "bottomleft",
  ...
)

Arguments

data	The data used to build the biplot
center	Column centering the data (default = TRUE). If center is TRUE then centering is done by subtracting the column means (omitting NA's) of x from their corresponding columns, and if center is FALSE, no centering is done.
scale	Scaling the data (default = FALSE). If scale is TRUE then scaling is done by dividing the (centered) columns of x by their standard deviations if center is TRUE, and the root mean square otherwise. If scale is FALSE, no scaling is done.
pcx	Which principal component to plot on the X-axis (default = 1)
pcy	Which principal component to plot on the Y-axis (default = 2)
groups	A vector from which the unique values are used to color the observations
col	Vector of colors, to color observations. Needs to be equal to the number of unique values of groups variable. If no groups is defined then all points will have the defined color.
pch	Either an integer specifying a symbol or a single character to be used as the default in plotting points. See points for possible values and their interpretation.
ellipse	Whether to add confidence ellipses to the different groups
ellipse.alpha	Alpha transparency value for the fill color (0 = transparent, 1 = opaque)
ellipse.conf	Confidence limit for ellipses, e.g. 0.68. If given, the corresponding sd or se is multiplied with the corresponding value found from the Chi-squared distribution with 2df.
ellipse.lwd	Line width of ellipse border
arrow.options	List to define options for the variable arrows (for all options see arrows ). Needs to be defined as a list, e.g. arrows.options = list(angle = 0.15, col = "blue"), errors could occur if a vector is used.
label.options	List to define options for the variable labels (for all options see text ). Needs to be defined as a list, e.g. label.options = list(cex = 1.2, col = "red"), errors could occur if a vector is used.
abbrev	Whether to abbreviate the variable names
circle	Whether to add a unit circle. Only applies if data is scaled!
circle.options	List to define options for the unit circle (for all options see polygon ). Needs to be defined as a list, e.g. circle.options = list(lty = "dashed", col = "grey"), errors could occur if a vector is used.
legend	Whether to add a legend
legend.pos	Position of the legend
...	Other graphical parameters, see plot for more details.

Examples

  data(iris)
  pca.biplot(iris[1:4])
  pca.biplot(iris[,-5], col = c("#00AFBB", "#E7B800", "#FC4E07"), groups = iris$Species, 
       legend = F, arrow.options = list(col="blue", angle = 20, length = 0.15))
  pca.biplot(iris[,-5], scale = T, col = c("#00AFBB", "#E7B800", "#FC4E07"), groups = iris$Species, 
       ellipse = T, pch = 16, legend.pos = 'topright')

StefaanVerwimp/Biplot documentation built on Feb. 10, 2021, 9:37 a.m.