ggbiplot {TCGAbiolinks} | R Documentation

## Biplot for Principal Components using ggplot2

### Description

Biplot for Principal Components using ggplot2

### Usage

    ggbiplot(pcobj, choices = 1:2, scale = 1, pc.biplot = TRUE,
      obs.scale = 1 - scale, var.scale = scale, groups = NULL,
      ellipse = FALSE, ellipse.prob = 0.68, labels = NULL,
      labels.size = 3, alpha = 1, var.axes = TRUE, circle = FALSE,
      circle.prob = 0.69, varname.size = 3, varname.adjust = 1.5,
      varname.abbrev = FALSE)

### Arguments

`pcobj` | an object returned by prcomp() or princomp()
`choices` | which PCs to plot
`scale` | covariance biplot (scale = 1), form biplot (scale = 0). When scale = 1, the inner product between the variables approximates the covariance and the distance between the points approximates the Mahalanobis distance.
`pc.biplot` | for compatibility with biplot.princomp()
`obs.scale` | scale factor to apply to observations
`var.scale` | scale factor to apply to variables
`groups` | optional factor variable indicating the groups that the observations belong to. If provided the points will be colored according to groups
`ellipse` | draw a normal data ellipse for each group?
`ellipse.prob` | size of the ellipse in Normal probability
`labels` | optional vector of labels for the observations
`labels.size` | size of the text used for the labels
`alpha` | alpha transparency value for the points (0 = transparent, 1 = opaque)
`var.axes` | draw arrows for the variables?
`circle` | draw a correlation circle? (only applies when prcomp was called with scale = TRUE and when var.scale = 1)
`circle.prob` | definition of circle.prob
`varname.size` | size of the text for variable names
`varname.adjust` | adjustment factor the placement of the variable names, >= 1 means farther from the arrow
`varname.abbrev` | whether or not to abbreviate the variable names

### Value

a ggplot2 plot

### Author(s)

Vincent Q. Vu.

[Package TCGAbiolinks version 2.12.6 Index]