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

In pca3d: Three Dimensional PCA Plots

Description

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

Usage

pca2d(
  pca,
  components = 1:2,
  col = NULL,
  title = NULL,
  new = FALSE,
  axes.color = "black",
  bg = "white",
  radius = 1,
  group = NULL,
  shape = NULL,
  palette = NULL,
  fancy = FALSE,
  biplot = FALSE,
  biplot.vars = 5,
  legend = NULL,
  show.scale = FALSE,
  show.labels = FALSE,
  labels.col = "black",
  show.axes = TRUE,
  show.axe.titles = TRUE,
  axe.titles = NULL,
  show.plane = TRUE,
  show.shadows = FALSE,
  show.centroids = FALSE,
  show.group.labels = FALSE,
  show.ellipses = FALSE,
  ellipse.ci = 0.95,
  ...
)

pca3d(
  pca,
  components = 1:3,
  col = NULL,
  title = NULL,
  new = FALSE,
  axes.color = "grey",
  bg = "white",
  radius = 1,
  group = NULL,
  shape = NULL,
  palette = NULL,
  fancy = FALSE,
  biplot = FALSE,
  biplot.vars = 5,
  legend = NULL,
  show.scale = FALSE,
  show.labels = FALSE,
  labels.col = "black",
  show.axes = TRUE,
  show.axe.titles = TRUE,
  axe.titles = NULL,
  show.plane = TRUE,
  show.shadows = FALSE,
  show.centroids = FALSE,
  show.group.labels = FALSE,
  show.shapes = TRUE,
  show.ellipses = FALSE,
  ellipse.ci = 0.95
)

Arguments

pca	Either a prcomp object or a matrix with at least three columns
components	Vector of length 3 (pca3d) or 2 (pca2d) 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
new	Use TRUE to open a new window
axes.color	Axis color This option has no effect in pca2d.
bg	Background color
radius	Scaling item for the size of points to be shown. In pca2d, this corresponds to the cex parameter.
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. In pca2d, the parameter is passed directly on to the pch option of the points() function.
palette	Specifies the color palette when colors are automatically assigned to the groups. See Details.
fancy	set show.labels, show.shadows, show.centroids and show.group.labels to TRUE.
biplot	Specify whether to show a biplot (see section ‘biplots’ below)
biplot.vars	Specify which loading to show on the biplot (see section ‘biplots’ below)
legend	If NULL, no legend will be drawn. Otherwise the value specifies the legend position in a form accepted by legend and legend3d.
show.scale	TRUE for showing a numeric scale at the edges of the plot. This option has no effect in pca2d.
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. This option has no effect in pca2d.
show.axe.titles	If TRUE, show axe titles (PC 1, PC 2 etc.) This option has no effect in pca2d.
axe.titles	A vector with two (pca2d) or three (pca3d) values containing the axe titles (corresponds to xlab and ylab in regular plot). If missing, but show.axe.titles is TRUE, axe titles will be generated automatically.
show.plane	If TRUE, show a grey horizontal plane at y = 0. This option has no effect in pca2d.
show.shadows	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. In pca2d, for each sample at (x,y), a grey line is drawn from (x,y) to (x,0).
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.
show.group.labels	Either TRUTH/FALSE or a vector equal to the number of unique values in the group parameter. If set, labels for each of the defined group will be shown at the group's centroid. If the value of the parameter is TRUE, then the group names will be taken from the group parameter. Otherwise, the values from this parameter will be used.
show.ellipses	A TRUTH/FALSE value indicating whether to show confidence interval ellipses or ellipsoids around each defined group
ellipse.ci	The confidence level of a pairwise confidence region for the CI. The default is 0.95, for a 95 the size of the ellipse being plotted.
...	For pca2d, any further argument will be passed on to the points() function.
show.shapes	A TRUTH/FALSE value indicating whether the different symbols (shapes) for the shown data points should be plotted (default TRUE).

Details

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

pca2d is the 2D counterpart. It creates a regular, two-dimensional plot on the standard graphic device. However, it takes exactly the same options as pca3d, such that it is easy to create 2D variants of the 3D graph.

Often, PCA visualisation requires using different symbols and colors for different groups of data. pca3d() and pca2d() aim at creating reasonable defaults, such that a simple call with two parameters – the pca object and the vector with group assignments of the samples – is sufficient for a basic diagnosis.

Value

Both pca2d and pca3d return invisibly a data frame which can be used to generate a legend for the figure. The data frame has as many rows as there are groups, and column with the group name, assigned color and assigned shape.

Biplots

If option biplot is TRUE, a biplot showing both the PCA results (samples) and variables is shown. This corresponds to the biplot function which works for the prcomp class objects. However, a biplot showing all variable loadings will be unreadable if the data is highly dimensional (for example, gene expression data). Therefore, the option biplot.vars specifies which variables are shown on the biplot.

If biplot.vars is a vector of length larger than one, it will be interpreted as a direct selection of the variables to be shown; for example, for a prcomp object pca, the variable selection will happen through pca$rotation[biplot.vars,].

If biplot.vars is a single number, then for each of the components shown, a number of variables equal to biplot.vars with the highest absolute loadings will be shown on the biplot.

Examples

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

  pca3d( pca, group= metabo[,1] )
  pca2d( pca, group= metabo[,1] )

  ## a bit more fancy:
  ## black background, white axes,
  ## centroids
  pca3d( pca, group= metabo[,1], 
    fancy= TRUE, bg= "black", 
    axes.color= "white", new= TRUE )

Example output

Warning messages:
1: In rgl.init(initValue, onlyNULL) : RGL: unable to open X11 display
2: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'. 
[1] 0.3439618 0.4500414 0.2818377
Creating new device
[1] 0.3439618 0.4500414 0.2818377
Creating new device

pca3d documentation built on Oct. 23, 2020, 8:26 p.m.