BP_Plot_Scores: BP_Plot_Scores

In PannetonB/inspectrar: GWidgets2/RGtk2 GUI for viewing and modeling spectroscopy data

BP_Plot_Scores

Description

Generates a biplot of scores from PCA with color coding of points, point labels and ellipses around data groups. Returns some parameters for easy replotting when zooming for example. If ax1 and ax2 are identical, plots a histogram of scores.

Usage

BP_Plot_Scores(
  ax1,
  ax2 = NULL,
  pcs,
  frac,
  xlimits = NULL,
  ylimits = NULL,
  colorby = rep(2, length(ax1)),
  pt.label = NULL,
  ell_option
)

Arguments

ax1	horizontal axis value of scores
ax2	vertical axis value of scores
pcs	2 element vector giving the PC number for ax1 and ax2 respectively for axis labelling
frac	2 element vector giving the % variance explained for PC on ax1 and ax2 respectively. For axis labelling.
xlimits	2 element vector giving the minimum and maximum value of the horizontal axis.
ylimits	2 element vector giving the minimum and maximum value of the vertical axis.
colorby	class for color coding of points. Default is all blue. When default, no legend is plotted.
pt.label	label for points. NA is used to skip a labels.
ell_option	option for plotting confidence ellipse around groups of points. "None", "0.50" or "0.95" Will be done only if there is more than one group defined by colorby.

Value

A list with the following elements:

• Xsc,Ysc : x and y values of all scores plotted.

• pcs : number of x and y axis principal comp.

• X_Lim, Y_Lim : xlim and ylim of current plot.

• colorby : class for color coding of points.

• pt.label : label for points. NA is used to skip a labels.

• ell_option : option for plotting confidence ellipse around groups of points. "None", "0.50" or "0.95" Will be done only if there is more than one group.

Examples

 BP_Plot_Scores(ax1=c(rnorm(20,10,2),rnorm(20,20,3)), ax2=rnorm(40,5,3),
                pcs=c(1,2), frac= c(81.2,9.8),
                colorby=as.factor(c(rep("Cl1",20),rep("Cl2",20))),
                ell_option="0.5")
                

PannetonB/inspectrar documentation built on Feb. 4, 2023, 1:57 p.m.