DrawScores: Scores plots

In FranceschiniS/LMWiRe: R Routines for Linear Model with Wide Response

Description

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

Usage

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)

Arguments

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.

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('UCH')
PCA.res = SVDforPCA(UCH$outcomes)

DrawScores(PCA.res,
  type.obj = 'PCA',
  main = 'PCA score plot for UCH dataset', axes =c(1,2))

FranceschiniS/LMWiRe documentation built on Oct. 30, 2019, 6:20 p.m.