DrawSL: Scores and Loadings plots

In ManonMartin/MBXUCL: R Routines for metabolomic data

Description

Draws scores and Loadings plots for PCA analysis derived from the SVDforPCA function.

Usage

DrawSL(
  obj,
  type.obj = c("PCA", "PLSDA", "OPLSDA"),
  drawNames = TRUE,
  createWindow = FALSE,
  main = NULL,
  class = NULL,
  axes = c(1, 2),
  type.graph = c("scores", "loadings"),
  loadingstype = c("l", "p", "s"),
  num.stacked = 4,
  xlab = NULL,
  ylab = NULL,
  ang = 0,
  xaxis = c("numerical", "character"),
  nxaxis = 10
)

Arguments

obj	The objects resulting from a PCA analysis with the SVDforPCA function.
type.obj	The type of object to be plotted.
drawNames	If TRUE, will show the observations names on the Scores plot.
createWindow	If TRUE, will create a new window for the plot.
main	Plot title. If NULL, default title is provided.
class	Optional character or numeric vector giving the class of the observations.
axes	Numerical vector indicating the PC axes that are drawn. Only the two first values are considered for scores plot. See details
type.graph	The type of plot, either 'scores' or 'loadings'
loadingstype	The type of Loadings plot, either a line plot ('l'), points ('p') or segments ('s').
num.stacked	Number of stacked plots if type is 'loadings'.
xlab	Label for the x-axis.
ylab	Label for the y-axis.
ang	Angle to rotate the x axis labels for a better visualisation.
xaxis	Specify if the xaxis is numerical or character
nxaxis	Number of thick marks on the xaxis for a character x variable

Details

If type.obj is 'OPLSDA', axes = 1 represents the predictive score vector, axes = 2 represents the first orthogonal score vector, etc.

Value

A score or loading plot in the current device.

Examples

data('HumanSerum')
res.PCA = SVDforPCA(HumanSerumSpectra)
class = ClassHS

DrawSL(res.PCA, drawNames=TRUE, type.obj = 'PCA',
createWindow=FALSE, main = 'PCA score plot for HumanSerum dataset',
  class = class, axes =c(1,2), type.graph ='scores')

DrawSL(res.PCA, drawNames=TRUE, type.obj = 'PCA',
createWindow=FALSE, main = 'PCA loadings plot for HumanSerum dataset',
   axes = 1, type.graph ='loadings', loadingstype='l')

ManonMartin/MBXUCL documentation built on Nov. 26, 2021, 8:45 p.m.