Family picture of shapes

Plots all the outlines, on the same graph, from a Coo (Out, Opn or Ldk) object.

Usage

# S3 method for Coo
stack(
  x,
  cols,
  borders,
  fac,
  palette = col_summer,
  coo_sample = 120,
  points = FALSE,
  first.point = TRUE,
  centroid = TRUE,
  ldk = TRUE,
  ldk_pch = 3,
  ldk_col = "#FF000055",
  ldk_cex = 0.5,
  ldk_links = FALSE,
  ldk_confell = FALSE,
  ldk_contour = FALSE,
  ldk_chull = FALSE,
  ldk_labels = FALSE,
  xy.axis = TRUE,
  title = substitute(x),
  ...
)

# S3 method for Ldk
stack(
  x,
  cols,
  borders,
  first.point = TRUE,
  centroid = TRUE,
  ldk = TRUE,
  ldk_pch = 20,
  ldk_col = col_alpha("#000000", 0.5),
  ldk_cex = 0.3,
  meanshape = FALSE,
  meanshape_col = "#FF0000",
  ldk_links = FALSE,
  ldk_confell = FALSE,
  ldk_contour = FALSE,
  ldk_chull = FALSE,
  ldk_labels = FALSE,
  slidings = TRUE,
  slidings_pch = "",
  xy.axis = TRUE,
  title = substitute(x),
  ...
)

Arguments

x: The Coo object to plot.
cols: A vector of colors for drawing the outlines. Either a single value or of length exactly equals to the number of coordinates.
borders: A vector of colors for drawing the borders. Either a single value or of length exactly equals to the number of coordinates.
fac: a factor within the $fac slot for colors
palette: a color palette to use when fac is provided
coo_sample: if not NULL the number of point per shape to display (to plot quickly)
points: logical whether to draw or not points
first.point: logical whether to draw or not the first point
centroid: logical whether to draw or not the centroid
ldk: logical. Whether to display landmarks (if any).
ldk_pch: pch for these landmarks
ldk_col: color for these landmarks
ldk_cex: cex for these landmarks
ldk_links: logical whether to draw links (of the mean shape)
ldk_confell: logical whether to draw conf ellipses
ldk_contour: logical whether to draw contour lines
ldk_chull: logical whether to draw convex hull
ldk_labels: logical whether to draw landmark labels
xy.axis: whether to draw or not the x and y axes
title: a title for the plot. The name of the Coo by default
...: further arguments to be passed to coo_plot
meanshape: logical whether to add meanshape related stuff (below)
meanshape_col: a color for everything meanshape
slidings: logical whether to draw slidings semi landmarks
slidings_pch: pch for semi landmarks

Value

a plot

Examples

# \donttest{
stack(bot)

bot.f <- efourier(bot, 12)
#> 'norm=TRUE' is used and this may be troublesome. See ?efourier #Details
stack(bot.f)
#> Warning: non-vector elements will be ignored
#> [1] ind
#> <0 rows> (or 0-length row.names)
stack(mosquito, borders='#1A1A1A22', first.point=FALSE)

stack(hearts)

stack(hearts, ldk=FALSE)

stack(hearts, borders='#1A1A1A22', ldk=TRUE, ldk_col=col_summer(4), ldk_pch=20)

stack(hearts, fac="aut", palette=col_sari)


chaffal <- fgProcrustes(chaff)
#> iteration:  1 	gain: 75173 
#> iteration:  2 	gain: 0.037814 
#> iteration:  3 	gain: 0.0090566 
#> iteration:  4 	gain: 0.00034224 
#> iteration:  5 	gain: 0.0069657 
#> iteration:  6 	gain: 0.002451 
#> iteration:  7 	gain: 0.0006129 
#> iteration:  8 	gain: 4.8815e-05 
#> iteration:  9 	gain: 0.00046668 
#> iteration:  10 	gain: 0.00018849 
#> iteration:  11 	gain: 2.4521e-05 
#> iteration:  12 	gain: 2.9766e-06 
#> iteration:  13 	gain: 2.4553e-05 
#> iteration:  14 	gain: 6.3825e-06 
#> iteration:  15 	gain: 5.1105e-06 
#> iteration:  16 	gain: 8.2596e-07 
#> iteration:  17 	gain: 2.8678e-06 
#> iteration:  18 	gain: 2.0472e-06 
#> iteration:  19 	gain: 6.5232e-07 
#> iteration:  20 	gain: 1.1298e-07 
#> iteration:  21 	gain: 1.3908e-07 
#> iteration:  22 	gain: 2.8327e-07 
#> iteration:  23 	gain: 2.1788e-07 
#> iteration:  24 	gain: 4.5583e-08 
#> iteration:  25 	gain: 7.0497e-08 
#> iteration:  26 	gain: 8.9792e-08 
#> iteration:  27 	gain: 5.538e-08 
#> iteration:  28 	gain: 1.2621e-08 
#> iteration:  29 	gain: 1.503e-08 
#> iteration:  30 	gain: 2.2108e-08 
#> iteration:  31 	gain: 1.4865e-08 
#> iteration:  32 	gain: 3.7216e-09 
#> iteration:  33 	gain: 3.8289e-09 
#> iteration:  34 	gain: 5.7787e-09 
#> iteration:  35 	gain: 3.9287e-09 
#> iteration:  36 	gain: 1.0587e-09 
#> iteration:  37 	gain: 9.2591e-10 
#> iteration:  38 	gain: 1.4847e-09 
#> iteration:  39 	gain: 1.039e-09 
#> iteration:  40 	gain: 2.9925e-10 
#> iteration:  41 	gain: 2.2588e-10 
#> iteration:  42 	gain: 3.8255e-10 
#> iteration:  43 	gain: 2.7403e-10 
#> iteration:  44 	gain: 8.3666e-11 
stack(chaffal, slidings=FALSE)

stack(chaffal, meanshape=TRUE, meanshape_col="blue")

# }

Usage

Arguments

Value

See also

Examples