MVP.PCAplot function

PCA Plot

MVP.PCAplot(
  PCA,
  memo = "MVP",
  col = NULL,
  pch = NULL,
  class = NULL,
  legend.pos = "topright",
  Ncluster = 1,
  plot3D = FALSE,
  file.type = "pdf",
  dpi = 300,
  box = FALSE,
  file.output = TRUE,
  outpath = getwd(),
  verbose = TRUE
)

Arguments

• PCA: Principal component analysis result, 2-column matrix

• memo: the prefix of the output image file.

• col: colors for each cluster

• pch: Either an integer specifying a symbol or a single character to be used as the default in plotting points. See points

  for possible values and their interpretation. Note that only integers and single-character strings can be set as a graphics parameter (and not NA nor NULL).

• class: the class of all individuals, for example: "breed", "location"

• legend.pos: position of legend. default is "topright"

• Ncluster: cluster number

• plot3D: (DEPRECATED)if TRUE, plot PC figure in 3D format, it can be only used in windows and mac operation system, "rgl" package should be installed beforehead

• file.type: Character. Options are jpg, pdf, and tiff

• dpi: Number. Dots per inch for .jpg and .tiff files

• box: Logical value. If TRUE, the border line of Manhattan plot will be added

• file.output: Logical value. If TRUE, the figures will be generated.

• outpath: Effective only when file.output = TRUE, determines the path of the output file

• verbose: whether to print detail.

Returns

Output file: MVP.PCA_2D.

Examples

genoPath <- system.file("extdata", "06_mvp-impute", "mvp.imp.geno.desc", package = "rMVP")
geno <- attach.big.matrix(genoPath)
pca <- MVP.PCA(M=geno, cpu=1)

MVP.PCAplot(PCA=pca, Ncluster=3, class=NULL, 
    col=c("red", "green", "yellow"), file.output=FALSE, pch=19)