pca3d (version 0.1)

pca3d-package: Show a three-dimensional plot of a prcomp object

Description

Show a three-dimensional plot of a prcomp object or a matrix, using different symbols and colors for groups of data

Usage

pca3d(pca, components = 1:3, col = "grey", title = NULL, offset = 50, new = FALSE, 
  axes.color = "black", bg = "white", radius = NULL, 
  group = NULL, shape = "sphere", show.scale = FALSE, 
  show.labels = FALSE, labels.col = "black", show.axes = T, 
  show.axe.titles = T, show.plane = T, show.shades = F, show.centroids = F)

Arguments

pca

Either a prcomp object or a matrix with at least three columns

components

Vector of length 3 containing the components to be shown

col

Either a single value or a vector of length equal to number of rows, containing color definitions for the plot points to be shown

title

Window title

offset

offset

new

Use TRUE to open a new window

axes.color

Axis color

bg

Background color

radius

Scaling item for the size of points to be shown

group

either NULL or a factor of length equal to number of rows. Factor levels can be used to automatically generate symbols and colors for the points shown

shape

Either a single value or a character vector describing the shapes to be used when drawing data points. Allowed shapes are: sphere, tetrahaedron and cube, and may be abbreviated.

show.scale

TRUE for showing a numeric scale at the edges of the plot.

show.labels

TRUE for showing labels (taken from the coordinate matrix or the prcomp object). Alternatively, a vector with labels to be shown next to the data points.

labels.col

Single value or vector describing the colors of the labels.

show.axes

TRUE to show the axes.

show.axe.titles

If TRUE, show axe titles (PC 1, PC 2 etc.)

show.plane

If TRUE, show a grey horizontal plane at y = 0

show.shades

If TRUE, show a "lollipop" representation of the points on the y = 0 plane: a vertical line joining the data point with the plane and a shadow.

show.centroids

If TRUE and the group variable is defined, show cluster centroids (using apropriate group symbols) and lines from each data point to the corresponding centroid.

Value

• No value is returned.

Details

pca3d shows a three dimensional representation of a PCA object or any other matrix. It uses the rgl package for rendering.

Examples

data( metabo )
  pca <- prcomp( metabo[,-1], scale.= TRUE )

  pca3d( pca, group= metabo[,1] )