pile: Graphical pile of shapes

In Momocs: Morphometrics using R

Graphical pile of shapes

Description

Pile all shapes in the same graphical window. Useful to check their normalization in terms of size, position, rotation, first point, etc. It is, essentially, a shortcut around paper + drawers of the grindr family.

Usage

pile(coo, f, sample, subset, pal, paper_fun, draw_fun, transp, ...)

## Default S3 method:
pile(
  coo,
  f,
  sample,
  subset,
  pal = pal_qual,
  paper_fun = paper,
  draw_fun = draw_curves,
  transp = 0,
  ...
)

## S3 method for class 'list'
pile(
  coo,
  f,
  sample = 64,
  subset = 1000,
  pal = pal_qual,
  paper_fun = paper,
  draw_fun = draw_curves,
  transp = 0,
  ...
)

## S3 method for class 'array'
pile(
  coo,
  f,
  sample = 64,
  subset = 1000,
  pal = pal_qual,
  paper_fun = paper,
  draw_fun = draw_landmarks,
  transp = 0,
  ...
)

## S3 method for class 'Out'
pile(
  coo,
  f,
  sample = 64,
  subset = 1000,
  pal = pal_qual,
  paper_fun = paper,
  draw_fun = draw_outlines,
  transp = 0,
  ...
)

## S3 method for class 'Opn'
pile(
  coo,
  f,
  sample = 64,
  subset = 1000,
  pal = pal_qual,
  paper_fun = paper,
  draw_fun = draw_curves,
  transp = 0,
  ...
)

## S3 method for class 'Ldk'
pile(
  coo,
  f,
  sample = 64,
  subset = 1000,
  pal = pal_qual,
  paper_fun = paper,
  draw_fun = draw_landmarks,
  transp = 0,
  ...
)

Arguments

coo	a single shape or any Coo object
f	factor specification
sample	numeric number of points to coo_sample if the number of shapes is > 1000 (default: 64). If non-numeric (eg FALSE) do not sample.
subset	numeric only draw this number of (randomly chosen) shapes if the number of shapes is > 1000 (default: 1000) If non-numeric (eg FALSE) do not sample.
pal	palette among palettes (default: pal_qual)
paper_fun	a papers function (default: paper)
draw_fun	one of drawers for pile.list
transp	numeric for transparency (default:adjusted, min:0, max=0)
...	more arguments to feed the core drawer, depending on the object

Details

Large Coo are sampled, both in terms of the number of shapes and of points to drawn.

Value

a plot

Note

A variation of this plot was called stack before ⁠Momocs 1.2.5⁠

See Also

Other grindr: drawers, layers_morphospace, layers, mosaic_engine(), papers, plot_LDA(), plot_NMDS(), plot_PCA()

Examples

# all Coo are supported with sensible defaults
pile(bot)    # outlines
pile(olea, ~var, pal=pal_qual_Dark2, paper_fun=paper_grid)   # curves
pile(wings)  # landmarks

# you can continue the pipe with compatible drawers
pile(bot, trans=0.9) %>% draw_centroid

# if you are not happy with this, build your own !
# eg see Momocs::pile.Out (no quotes)

my_pile <- function(x, col_labels="red", transp=0.5){
    x %>% paper_chess(n=100) %>%
          draw_landmarks(transp=transp) %>%
          draw_labels(col=col_labels)
}
# using it
wings %>% my_pile(transp=3/4)

 # and as gridr functions propagate, you can even continue:
 wings %>% my_pile() %>% draw_centroid(col="blue", cex=5)

 # method on lists
 bot$coo %>% pile

 # it can be tuned when we have a list of landmarks with:
 wings$coo %>% pile(draw_fun=draw_landmarks)

 # or on arrays (turn for draw_landmarks)
 wings$coo %>% l2a %>% #we now have an array
     pile

Momocs documentation built on Nov. 13, 2023, 5:07 p.m.