biplot_color {scone} | R Documentation

## Function for biplotting with no point labels and with points color-coded according to a quantitative variable. For example: the rank of normalization performance.

### Description

This function implements biplot for `prcomp` objects.

### Usage

    biplot_color(
      x,
      y,
      rank = TRUE,
      ties_method = c("max", "min", "first", "last", "random"),
      choices = 1:2,
      expand = 1,
      ...
    )

### Arguments

`x` | `prcomp` object.
`y` | numeric. Quantitative values used to color the points. If rank is FALSE, all values must be positive integers and less than or equal to the length of y.
`rank` | logical. If TRUE (default) y will be transformed by the rank() function
`ties_method` | character. ties.method used by the rank() function
`choices` | numeric. 2 principal components to plot. Default to first two PCs.
`expand` | numeric. value used to adjust the spread of the arrows relative to the points.
`...` | arguments passed to plot.

### Value

Invisibly returns scaled point coordinates used in plot.

### Examples

    mat <- matrix(rnorm(1000), ncol=10)
    colnames(mat) <- paste("X", 1:ncol(mat), sep="")

    pc <- prcomp(mat)

    biplot_color(pc, rank(pc$x[,1]))

[Package scone version 1.18.0 Index]