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Biplot for PCA Objects (Enhanced with ggrepel)

biplot.pca.Rd

Creates a 2D biplot for a pca object, using ggplot2 and ggrepel to show both sample scores (observations) and variable loadings (arrows).

Usage

# S3 method for class 'pca'
biplot(
  x,
  y = NULL,
  dims = c(1, 2),
  scale_arrows = 2,
  alpha_points = 0.6,
  point_size = 2,
  point_labels = NULL,
  var_labels = NULL,
  arrow_color = "red",
  text_color = "red",
  repel_points = TRUE,
  repel_vars = FALSE,
  ...
)

Arguments

x

A pca object returned by pca.

y

(ignored) Placeholder to match biplot(x, y, ...) signature.

dims

A length-2 integer vector specifying which principal components to plot on the x and y axes. Defaults to c(1, 2).

scale_arrows

A numeric factor to scale the variable loadings (arrows). Default is 2.

alpha_points

Transparency level for the sample points. Default is 0.6.

point_size

Size for the sample points. Default is 2.

point_labels

Optional character vector of labels for the sample points. If NULL, rownames of the scores matrix are used if available; otherwise numeric indices.

var_labels

Optional character vector of variable names (columns in the original data). If NULL, rownames of x\$v are used if available; otherwise "Var1", "Var2", etc.

arrow_color

Color for the loading arrows. Default is "red".

text_color

Color for the variable label text. Default is "red".

repel_points

Logical; if TRUE, repel sample labels using geom_text_repel. Default is TRUE.

repel_vars

Logical; if TRUE, repel variable labels using geom_text_repel. Default is FALSE.

...

Additional arguments passed on to ggplot2 or ggrepel functions (if needed).

Value

A ggplot object.

Details

This function constructs a scatterplot of the PCA scores (observations) on two chosen components and overlays arrows for the loadings (variables). The arrow length and direction indicate how each variable contributes to those principal components. You can control arrow scaling with scale_arrows.

If your pca object includes an $explained_variance field (e.g., proportion of variance per component), those values will appear in the axis labels. Otherwise, the axes are labeled simply as "PC1", "PC2", etc.

Note: If you do not have ggrepel installed, you can set repel_points=FALSE and repel_vars=FALSE, or install ggrepel.

Examples

if (FALSE) { # \dontrun{
data(iris)
X <- as.matrix(iris[,1:4])
pca_res <- pca(X, ncomp=2)

# Enhanced biplot with repelled text
biplot(pca_res, repel_points=TRUE, repel_vars=TRUE)
} # }