Momocs (version 1.4.1)

plot.PCA: Plots Principal Component Analysis

Description

The Momocs' PCA plotter with morphospaces and many graphical options.

Usage

# S3 method for PCA
plot(
  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 = TRUE,
  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 = FALSE,
  conf.ellipsesax = c(0.5, 0.9),
  lty.ellipsesax = 1,
  lwd.ellipsesax = sqrt(2),
  chull = FALSE,
  chull.lty = 1,
  chull.filled = TRUE,
  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,
  ...
)

Value

a plot

Arguments

x

PCA, typically obtained with PCA

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

Details

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

See Also

plot.LDA

Examples

# \donttest{
bot.f <- efourier(bot, 12)
bot.p <- PCA(bot.f)

### Morphospace options
plot(bot.p, pos.shp="full")
plot(bot.p, pos.shp="range")
plot(bot.p, pos.shp="xy")
plot(bot.p, pos.shp="circle")
plot(bot.p, pos.shp="range_axes")
plot(bot.p, pos.shp="full_axes")

plot(bot.p, morpho=FALSE)

### Passing factors to plot.PCA
# 3 equivalent methods
plot(bot.p, "type")
plot(bot.p, 1)
plot(bot.p, ~type)

# let's create a dummy factor of the correct length
# and another added to the $fac with mutate
# and a numeric of the correct length
f <- factor(rep(letters[1:2], 20))
z <- factor(rep(LETTERS[1:2], 20))
bot %<>% mutate(cs=coo_centsize(.), z=z)
bp <- bot %>% efourier %>% PCA
# so bp contains type, cs (numeric) and z; not f
# yet f can be passed on the fly
plot(bp, f)
# numeric fac are allowed
plot(bp, "cs", cex=3, color.legend=TRUE)
# formula allows combinations of factors
plot(bp, ~type+z)

### other morphometric approaches works the same
# open curves
op <- npoly(olea, 5)
op.p <- PCA(op)
op.p
plot(op.p, ~ domes + var, morpho=TRUE) # use of formula

# landmarks
wp <- fgProcrustes(wings, tol=1e-4)
wpp <- PCA(wp)
wpp
plot(wpp, 1)

### Cosmetic options
# window
plot(bp, 1, zoom=2)
plot(bp, zoom=0.5)
plot(bp, center.origin=FALSE, grid=FALSE)

# colors
plot(bp, col="red") # globally
plot(bp, 1, col=c("#00FF00", "#0000FF")) # for every level
# a color vector of the right length
plot(bp, 1, col=rep(c("#00FF00", "#0000FF"), each=20))
# a color vector of the right length, mixign Rcolor names (not a good idea though)
plot(bp, 1, col=rep(c("#00FF00", "forestgreen"), each=20))


# ellipses
plot(bp, 1, conf.ellipsesax=2/3)
plot(bp, 1, ellipsesax=FALSE)
plot(bp, 1, ellipsesax=TRUE, ellipses=TRUE)

# stars
plot(bp, 1, stars=TRUE, ellipsesax=FALSE)

# convex hulls
plot(bp, 1, chull=TRUE)
plot(bp, 1, chull.lty=3)

# filled convex hulls
plot(bp, 1, chull.filled=TRUE)
plot(bp, 1, chull.filled.alpha = 0.8, chull.lty =1) # you can omit chull.filled=TRUE

# density kernel
plot(bp, 1, density=TRUE, contour=TRUE, lev.contour=10)

# delaunay
plot(bp, 1, delaunay=TRUE)

# loadings
flower %>% PCA %>% plot(1, loadings=TRUE)

# point/group labelling
plot(bp, 1, labelspoint=TRUE) # see options for abbreviations
plot(bp, 1, labelsgroup=TRUE) # see options for abbreviations

# clean axes, no rug, no border, random title
plot(bp, axisvar=FALSE, axisnames=FALSE, rug=FALSE, box=FALSE, title="random")

# no eigen
plot(bp, eigen=FALSE) # eigen cause troubles to graphical window
# eigen may causes troubles to the graphical window. you can try old.par = TRUE
# }