plotPCA: Generate PCA plot
In maize-genetics/rTASSEL: R Front-End for TASSEL

plotPCA

R Documentation

Generate PCA plot

Description

This function will generate a general 2D scatterplot for a given set of principal components.

Usage

plotPCA(
  pcaObj,
  x = 1,
  y = 2,
  cluster = FALSE,
  nClust = 2,
  metadata = NULL,
  mCol = NULL,
  interactive = FALSE,
  pointColor = "black"
)

Arguments

`pcaObj`	A `PCAResults` object containing eigenvalue data ( e.g `PC_Datum`).
`x`	Principal component number to plot on x-axis.
`y`	Principal component number to plot on y-axis.
`cluster`	Plot points by hierachical clustering groups? Defaults to `FALSE`.
`nClust`	Number of clusters to report.
`metadata`	A `data.frame` object of additional categorical information for each sample/taxa. Defaults to `NULL`.
`mCol`	What metadata column do you want to plot? Needs metadata object to work.
`interactive`	Do you want to produce an interactive visualization? Defaults to `FALSE`.
`pointColor`	color of non-categorical PCA data points.