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, 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.
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
center.origin
logical whether to center the plot onto the origin
zoom
to keep your distances
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 pos.shapes, one of
"range", "full", "circle", "xy", "range_axes", "full_axes". Or directly
a matrix of positions. See pos.shapes 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