plotScores {Rnmr1D}

plotScores

Description

Plots the two components defined by pc1, pc2 of the matrix of scores coming from a multivariable analysis, typically a Principal Component Analysis (PCA).

Usage

plotScores(
  data,
  pc1,
  pc2,
  samples,
  factor = NULL,
  cexlabel = 1.2,
  level = 0.95,
  xlim = NULL,
  ylim = NULL,
  col = NULL
)

Arguments

data

the matrix of scores coming from a multivariable analysis, typically a Principal Component Analysis (PCA)

pc1

the fist component of the matrix of variable loadings to be plotted.

pc2

the second component of the matrix of variable loadings to be plotted. as well as the levels of the experimental factors if specified in the input. See doProcessing or generateMetadata

samples

the samples matrix with the correspondence of the raw spectra,

factor

if not null, the name of one of the columns defining the factorial groups in the samples matrix at input

cexlabel

number indicating the amount by which plotting text and symbols should be scaled relative to the default.

level

confidence level for plotting the corresponding ellipse

xlim

gives the limit to be plotted of the first component

ylim

gives the limit to be plotted of the second component

col

colors vector for ellipses - automatically defined by default