Plot score and loading plot

Plot 2D PCA score and loading plots choosing the principal components.

Plot2DPCA(
  mRList = NULL,
  pcx = 1,
  pcy = 2,
  dirout = NULL,
  col_pal = NULL,
  col_by = "class",
  include_QC = FALSE,
  name_samples = FALSE,
  name_samples_cex = 0.8
)

Arguments

mRList

mRList object

pcx

Specify the principal component on the x-axis

pcy

Specify the principal component on the y-axis

dirout

output directory

col_pal

optional palette. It must match the number of levels of the factor indicated by col_by

col_by

(default class)

include_QC

(default TRUE)

name_samples

whether the names of samples should be added to each point

name_samples_cex

if name_samples is TRUE, specify here the size of the sample names