stack.Coo: Family picture of shapes
In vbonhomme/Momocs: Morphometrics using R

stack

R Documentation

Family picture of shapes

Description

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

Usage

## S3 method for class '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 class '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


stack(bot)
bot.f <- efourier(bot, 12)
stack(bot.f)
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)
stack(chaffal, slidings=FALSE)
stack(chaffal, meanshape=TRUE, meanshape_col="blue")

vbonhomme/Momocs documentation built on Nov. 13, 2023, 8:54 p.m.