plot_PC: Plot of principal components

In Rundmus/BAf-R_package: Binder Array data hanlding package in facility

Description

The plot of a pair of principal components is displayed for a matrix or a single BAf-class object. Colors or symbols of the points can be diffrentiated by the variable given in col_by or pch_by to assist to find hidden substructure of sample. The principal components were obtained by (prcomp) with scaling.

Usage

plot_PC(x, pc = c(1, 2), main = "", xlab, ylab, ...)

## S4 method for signature 'prcomp'
plot_PC(x, pc = c(1, 2), main = "", xlab, ylab, ...)

## S4 method for signature 'matrix'
plot_PC(x, pc = c(1, 2), main = "", xlab, ylab, ...)

## S4 method for signature 'BAf'
plot_PC(
  x,
  pc = c(1, 2),
  main = "",
  xlab,
  ylab,
  ...,
  col_by = NULL,
  pch_by = NULL,
  legend_arg = list(x = "topright")
)

Arguments

x	an object of the prcomp, matrix or BAf-class
pc	a vector that consists of two integer elements for two principal components
main, xlab, ylab	same as plot.default
...	pass to plot
col_by, pch_by	a name of a column in sI(x). Different color / symbols the points will have.
legend_arg	a list of parameters to be used in adding a legend. If NULL, skip to add legend

Value

plot_PC prcomp output object

Functions

• plot_PC,prcomp-method: The input is the output of 'prcomp'

• plot_PC,matrix-method: The input is a 'matrix'

• plot_PC,BAf-method: The input is a 'BAf' object

Author(s)

Mun-Gwan Hong [e-mail]

See Also

prcomp

Examples

data(sba)
plot_PC(sba)
plot_PC(sba, col_by= "plate")    # no legend
plot_PC(sba, col_by= "plate", pch_by= "sex", legend_arg= list())

Rundmus/BAf-R_package documentation built on May 18, 2020, 12:59 p.m.