man-roxygen/mr_pca_plot_param.r

In bpollner/aquap2: Multivariate Data Analysis Tools for R including Aquaphotomics Methods

#' @param do.pca Logical. If used in a plotting function, if PCA score / loading 
#'  plots should be plotted.
#' @param pca.colorBy NULL or character vector. Which class-variables 
#'  should be used for coloring the PCA score plot. Set to NULL for using all 
#'  available class variables for coloring.
#' @param pca.elci 'def' or numeric length one. The confidence interval for the
#'  ellipse to be drawn around groups in score plots. Leave at 'def' to read in 
#'  the default from the settings.r file; provide a numeric length one 
#'  (e.g. 0.95); or set to NULL for not drawing ellipses at all.
#' @param pca.elcolorBy Character vector or NULL. The variables to use for 
#'  plotting additional confidence intervall ellipses. Set to NULL for *not* 
#'  drawing additional CI-ellipses. Provide one variable (gets recycled) or a 
#'  vector with equal length as \code{pca.colorBy} to have the additional 
#'  CI-ellipses along these variables.
#' @param pca.what Character length one. What element of the PCA analysis to plot.
#'  Possible values are <%=r_listize(pv_pca_what)%>.
#' @param pca.sc Numeric length 2. Two PCs to be plotted against each other 
#'  in the score plots.
#' @param pca.sc.pairs Numeric vector of length >=2, indicating what PCs 
#'  to plot in the score pairs plot. Set to NULL for *not* plotting the pairs 
#'  plot.
#' @param pca.lo  Numeric vector of length >=2, indicating what PCs to plot in 
#'  the loadingplot.