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Plot A PCA Dimension

plot_pca_dims.Rd

Plots either the projection or the loadings (rotation) of "prcomp" object. This is a base function that is wrapped into driver parent functions in the plotting of principal components, most notably plot_rotation() and plot_projection().

Usage

plot_pca_dims(
  data.prcomp,
  value = c(NA, "rotation", "x"),
  dims,
  classes,
  main = sprintf("PCA Plot (%s)", ifelse(value == "x", "projection", value)),
  scores = NULL,
  col = NULL,
  xlab = NULL,
  ylab = NULL,
  legend_pos = "right",
  xlim = NULL,
  ylim = NULL,
  pt_cex = 2.5,
  pt_pch = 19,
  add_ellipse = FALSE,
  ...
)

Arguments

data.prcomp

A prcomp class object. Typically the object returned by prcomp2().

value

Character. The type of plot to be generated. For projection enter "x", for rotation enter "rotation".

dims

integer(2). Which dimensions to plot.

classes

Optional. A vector indicating the classes of observations (either features or samples) used for coloring the points, depending on whether a rotation or a projection is to be plotted. Must be the same length as the plot type, i.e. number of samples for projection and features for rotation.

main

character(1). A string containing the title for the plot.

scores

Optional. Statistical scores to pass through for the coloring of the points during plotting. If a training data set is passed and scores = NULL, then KS-distances (scores) will be calculated under the hood and used to determine point color. Can be either a single value (e.g. "red") or a vector of color values the same length as the number of observations. This overrides the point color assigned by classes above.

col

character(1). The color of the points. Can be either a single value (e.g. "red") or a vector of color values the same length as the number of observations. This parameter overrides the point colors determined by both the classes and scores parameters above.

xlab

character(1). A string indicating the label of the x axis.

ylab

character(1). A string indicating the label of the y axis.

legend_pos

character(1). Position of the legend, if plotted. Options include "left", "right", "bottom", or "top", or "none" if no legend is desired. Ignored if value = "r" (rotation) and classes are not specified.

xlim

numeric(2). Optional limits for the x-axis in the format c(0, 0).

ylim

Numeric. Optional limits for the y-axis in the format c(0, 0).

pt_cex

numeric(1). Character expansion for the points.

pt_pch

numeric(1). Shape of the points. Accepted values are 0-25.

add_ellipse

Logical. Should an ellipse be added to the rotation? Ignored if projection (value = "x").

...

Additional arguments passed to geom_point().

Value

A points plot of either the rotation or projection space.

See also

Other PCA plots: plot_projection(), plot_rotation(), screeplot_auc()

Author

Stu Field, Michael R. Mehan

Examples

# Prepare data
pca <- center_scale(pcapkg:::log10_ft(simdata), center = TRUE, scale = FALSE) |>
  feature_matrix() |>
  prcomp2()
scores <- withr::with_seed(101, rnorm(40))

# Rotation space, with scores to define point colors
plot_pca_dims(pca, value = "r", dims = 1:2L, classes = NULL,
              scores = rnorm(40))


# Projection space, with classes to define point colors
plot_pca_dims(pca, value = "x", dims = 1:2L,
              classes = simdata$class_response)