Plots Linear Discriminant Analysis

The Momocs' LDA plotter with many graphical options.

Usage

# S3 method for LDA
plot(
  x,
  fac = x$fac,
  xax = 1,
  yax = 2,
  points = TRUE,
  col = "#000000",
  pch = 20,
  cex = 0.5,
  palette = col_solarized,
  center.origin = FALSE,
  zoom = 1,
  xlim = NULL,
  ylim = NULL,
  bg = par("bg"),
  grid = TRUE,
  nb.grids = 3,
  morphospace = FALSE,
  pos.shp = c("range", "full", "circle", "xy", "range_axes", "full_axes")[1],
  amp.shp = 1,
  size.shp = 1,
  nb.shp = 12,
  nr.shp = 6,
  nc.shp = 5,
  rotate.shp = 0,
  flipx.shp = FALSE,
  flipy.shp = FALSE,
  pts.shp = 60,
  border.shp = col_alpha("#000000", 0.5),
  lwd.shp = 1,
  col.shp = col_alpha("#000000", 0.95),
  stars = FALSE,
  ellipses = FALSE,
  conf.ellipses = 0.5,
  ellipsesax = TRUE,
  conf.ellipsesax = c(0.5, 0.9),
  lty.ellipsesax = 1,
  lwd.ellipsesax = sqrt(2),
  chull = FALSE,
  chull.lty = 1,
  chull.filled = FALSE,
  chull.filled.alpha = 0.92,
  density = FALSE,
  lev.density = 20,
  contour = FALSE,
  lev.contour = 3,
  n.kde2d = 100,
  delaunay = FALSE,
  loadings = FALSE,
  labelspoints = FALSE,
  col.labelspoints = par("fg"),
  cex.labelspoints = 0.6,
  abbreviate.labelspoints = TRUE,
  labelsgroups = TRUE,
  cex.labelsgroups = 0.8,
  rect.labelsgroups = FALSE,
  abbreviate.labelsgroups = FALSE,
  color.legend = FALSE,
  axisnames = TRUE,
  axisvar = TRUE,
  unit = FALSE,
  eigen = TRUE,
  rug = TRUE,
  title = substitute(x),
  box = TRUE,
  old.par = TRUE,
  ...
)

Arguments

x: an object of class "LDA", typically obtained with LDA
fac: name or the column id from the $fac slot, or a formula combining colum names from the $fac slot (cf. examples). A factor or a numeric of the same length can also be passed on the fly.
xax: the first PC axis
yax: the second PC axis
points: logical whether to plot points
col: a color for the points (either global, for every level of the fac or for every individual, see examples)
pch: a pch for the points (either global, for every level of the fac or for every individual, see examples)
cex: the size of the points
palette: a palette
center.origin: logical whether to center the plot onto the origin
zoom: to keep your distances
xlim: numeric of length two ; if provided along with ylim, the x and y lims to use
ylim: numeric of length two ; if provided along with xlim, the x and y lims to use
bg: color for the background
grid: logical whether to draw a grid
nb.grids: and how many of them
morphospace: logical whether to add the morphological space
pos.shp: passed to morphospace_positions, one of "range", "full", "circle", "xy", "range_axes", "full_axes". Or directly a matrix of positions. See morphospace_positions
amp.shp: amplification factor for shape deformation
size.shp: the size of the shapes
nb.shp: (pos.shp="circle") the number of shapes on the compass
nr.shp: (pos.shp="full" or "range) the number of shapes per row
nc.shp: (pos.shp="full" or "range) the number of shapes per column
rotate.shp: angle in radians to rotate shapes (if several methods, a vector of angles)
flipx.shp: same as above, whether to apply coo_flipx
flipy.shp: same as above, whether to apply coo_flipy
pts.shp: the number of points fro drawing shapes
border.shp: the border color of the shapes
lwd.shp: the line width for these shapes
col.shp: the color of the shapes
stars: logical whether to draw "stars"
ellipses: logical whether to draw confidence ellipses
conf.ellipses: numeric the quantile for the (bivariate gaussian) confidence ellipses
ellipsesax: logical whether to draw ellipse axes
conf.ellipsesax: one or more numeric, the quantiles for the (bivariate gaussian) ellipses axes
lty.ellipsesax: if yes, the lty with which to draw these axes
lwd.ellipsesax: if yes, one or more numeric for the line widths
chull: logical whether to draw a convex hull
chull.lty: if yes, its linetype
chull.filled: logical whether to add filled convex hulls
chull.filled.alpha: numeric alpha transparency
density: whether to add a 2d density kernel estimation (based on kde2d)
lev.density: if yes, the number of levels to plot (through image)
contour: whether to add contour lines based on 2d density kernel
lev.contour: if yes, the (approximate) number of lines to draw
n.kde2d: the number of bins for kde2d, ie the 'smoothness' of density kernel
delaunay: logical whether to add a delaunay 'mesh' between points
loadings: logical whether to add loadings for every variables
labelspoints: if TRUE rownames are used as labels, a colname from $fac can also be passed
col.labelspoints: a color for these labels, otherwise inherited from fac
cex.labelspoints: a cex for these labels
abbreviate.labelspoints: logical whether to abbreviate
labelsgroups: logical whether to add labels for groups
cex.labelsgroups: ifyes, a numeric for the size of the labels
rect.labelsgroups: logical whether to add a rectangle behind groups names
abbreviate.labelsgroups: logical, whether to abbreviate group names
color.legend: logical whether to add a (cheap) color legend for numeric fac
axisnames: logical whether to add PC names
axisvar: logical whether to draw the variance they explain
unit: logical whether to add plane unit
eigen: logical whether to draw a plot of the eigen values
rug: logical whether to add rug to margins
title: character a name for the plot
box: whether to draw a box around the plotting region
old.par: whether to restore the old par. Set it to FALSE if you want to reuse the graphical window.
...: useless here, just to fit the generic plot

Value

a plot

Details

Widely inspired by the "layers" philosophy behind graphical functions of the ade4 R package.

Note

Morphospaces are deprecated so far. 99% of the code is shared with plot.PCA waiting for a general rewriting of a multivariate plotter. See https://github.com/vbonhomme/Momocs/issues/121