visualize: Plot the ILDS with the relevant ILDS ighlighted

In Morpho: Calculations and Visualisations Related to Geometric Morphometrics

Plot the ILDS with the relevant ILDS ighlighted

Description

Plot the ILDS with the relevant ILDS ighlighted

Usage

visualize(x, ...)

## S3 method for class 'ILDSR2'
visualize(
  x,
  ref = TRUE,
  relcol = "red",
  rescol = "black",
  lwd = 1,
  cex = 2,
  col = "red",
  pch = 19,
  contractcol = c("red", "orange"),
  expandcol = c("blue", "cyan"),
  conftol = c(75, 50),
  useconf = TRUE,
  add = FALSE,
  plot.legend = FALSE,
  ngrid = 0,
  gridcol = "grey90",
  gridlty = 3,
  links = NULL,
  linkcol = "grey50",
  lollipop = TRUE,
  lollipopcol = "black",
  magnify = 1,
  ...
)

visualise(x, ...)

## S3 method for class 'ILDSR2'
visualise(
  x,
  ref = TRUE,
  relcol = "red",
  rescol = "black",
  lwd = 1,
  cex = 2,
  col = "red",
  pch = 19,
  contractcol = c("red", "orange"),
  expandcol = c("blue", "cyan"),
  conftol = c(75, 50),
  useconf = TRUE,
  add = FALSE,
  plot.legend = FALSE,
  ngrid = 0,
  gridcol = "grey90",
  gridlty = 3,
  links = NULL,
  linkcol = "grey50",
  lollipop = TRUE,
  lollipopcol = "black",
  magnify = 1,
  ...
)

Arguments

x	output of function ILDSR2
...	additional parameters passed to deformGrid2d / deformGrid3d.
ref	logical: if TRUE, the reference shape defined in ILDSR2 will be plotted. Otherwise the target is used. If ref=FALSE, the contraction and exxpansion will also be inverted
relcol	color of relevant ILDs
rescol	color of "irrelevant" ILDs
lwd	numeric: define line width. Relevant ILDs are displayed by 3*lwd.
cex	numeric: size of plot content
col	define color of landmarks
pch	define symbols used to plot landmarks in 2D plot.
contractcol	vector of colors for shortening ILDs, associated with confidence. Must be of length(contol).
expandcol	vector of colors for expanding ILDs, associated with confidence. Must be of length(contol).
conftol	vector: set thresholds for confidence coloring
useconf	logical: if TRUE, highlighting according to supported confidence of ILD is applied.
add	logical: if TRUE, plot is added to an existin one.
plot.legend	logical: if TRUE, a legend is added to the plots with information on the coloring scheme.
ngrid	integer: if ngrid > 0, a TPS grid is shown to display the spatial deformation from reference to target shape.
gridcol	color of TPS grid
gridlty	line type for TPS grid
links	integer vector or list containing multiple integer vectors or a k x 2 integer matrix where each row defines a single link: add information on how landmarks are linked (aka wireframe)
linkcol	color of wireframe defined by links
lollipop	logical: if TRUE, landmark displacement between reference and target is displayed as lollipop graph.
lollipopcol	color for lollipop handles
magnify	numeric: symmetrically increase differences between reference and target by that factor

Examples

## 3D Example
require(Morpho)
data(boneData)
proc <- procSym(boneLM)
groups <- name2factor(boneLM,which=3)
ilds <- ILDSR2(proc$rotated,groups,plot=FALSE,bg.rounds=0,wg.rounds=99)
visualize(ilds)

## 2D Example
require(shapes)
gor.dat <- bindArr(gorf.dat,gorm.dat,along=3)
sex <- factor(c(rep("f",30),rep("m",29)))
procg <- procSym(gor.dat)
ildsg <- ILDSR2(procg$rotated,sex,plot=FALSE,bg.rounds=0,wg.rounds=99,R2tol=.9)
visualize(ildsg,cex=2,pch=19)

## use custom color and thresholds
visualize(ildsg,cex=2,pch=19,confcol=rainbow(5),contractcol=c(0.9,0.6,0.4))

Morpho documentation built on Sept. 9, 2025, 5:46 p.m.