DrawScores: Scores plots
In ManonMartin/MBXUCL: R Routines for metabolomic data

Description Usage Arguments Details Value Examples

Draws scores plots for the SVDforPCA, PLSDA or OPLSDA functions.

DrawScores(
  obj,
  type.obj = c("PCA", "PLSDA", "OPLSDA"),
  drawNames = TRUE,
  createWindow = FALSE,
  main = NULL,
  color = NULL,
  pch = NULL,
  size = 1,
  cex.lab = 3,
  axes = c(1, 2),
  xlab = NULL,
  ylab = NULL,
  drawEllipses = FALSE,
  typeEl = "norm",
  levelEl = 0.9,
  drawPolygon = FALSE,
  noLegend = FALSE,
  legend_color_manual = NULL,
  legend_shape_manual = NULL
)

`obj`	The objects resulting from a PCA, PLSDA or OPLSDA analysis.
`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.
`color`	Optional character, factor or numeric vector giving the color of the observations. If `length(color)` = 1, the unique color is kept for all the points.
`pch`	Optional character, factor or numeric vector giving the pch of the observations.
`size`	The points size.
`cex.lab`	The size of points labels.
`axes`	Numerical vector indicating the PC axes that are drawn. Only the two first values are considered for scores plot. See details#' @param num.stacked Number of stacked plots if `type` is `'loadings'`.
`xlab`	Label for the x-axis.
`ylab`	Label for the y-axis.
`drawEllipses`	If `TRUE`, will draw ellipses with the `ggplot2::stat_ellipse` with groups coresponding to the color vector.
`typeEl`	The type of ellipse, either "norm" (multivariate normal distribution), "t" (multivariate t-distribution) and "euclid" draws a circle with the radius equal to level, representing the euclidean distance from the center.
`levelEl`	The confidence level at which to draw an ellipse.
`drawPolygon`	If `TRUE`, will relate the points linked to the same group (color vector)
`noLegend`	If `TRUE`, no legend is drawn.
`legend_color_manual`	If not `NULL`, a named character vector giving manually the colors to be drawn, named with the levels of the color vector.
`legend_shape_manual`	If not `NULL`, a named character vector giving manually the shapes to be drawn, named with the levels of the pch vector.

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

A score or loading plot in the current device.

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

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