Description Usage Arguments Details Note See Also Examples
The Momocs' LDA
plotter with many graphical options.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21  ## S3 method for class '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, ...)

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

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 
... 
useless here, just to fit the generic plot 
Widely inspired by the "layers" philosophy behind graphical functions of the ade4 R package.
Morphospaces are deprecated so far. 99 is shared with plot.PCA waiting for a general rewriting of a multivariate plotter. See https://github.com/vbonhomme/Momocs/issues/121
LDA, plot_CV, plot_CV2, plot.PCA.
1 2 3 4 5 6 7 
This is Momocs 1.1.6
Attaching package: 'Momocs'
The following object is masked from 'package:stats':
filter
The following object is masked from 'package:base':
table
Warning messages:
1: In rgl.init(initValue, onlyNULL) : RGL: unable to open X11 display
2: 'rgl_init' failed, running with rgl.useNULL = TRUE
3: .onUnload failed in unloadNamespace() for 'rgl', details:
call: fun(...)
error: object 'rgl_quit' not found
0.99 total variance
8 PC retained
NULL
0.99 total variance
8 PC retained
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