animdefo: animdefo
In deformetrics/deformetrics: R functions for shape analysis

Description Usage Arguments Author(s) Examples

This function save images of 2D the deformations of a reference 2d shape relatively to sequence(s) of shapes contained in "seqlist" argument; this can store from 1 to 4 sequences of shapes. Plots are saved in the working directory and can be combined in animated GIF using external softwares. By default the titles of each plot are "PC1", "PC2", "PC3", "PC4" but any title can be set (see examples). Heatmap is computed by default.

animdefo(mshape, seqlist, suffix = "anim", czlim = T, czlimw = F,
  linkss = NULL, linkst = NULL, colss = 1, colst = 2, lwds = 2,
  lwdt = 2, cexs = 0, cext = 0, displ = F, axtit = NULL, mag = 1,
  heat = T, mar = c(0, 0, 0.3, 0), mai = c(0, 0, 0.3, 0), oma = c(0, 0,
  3, 0), colors = c("blue4", "cyan2", "yellow", "red4"), alpha = 1,
  magrange = 1, exts = NULL, PB = NA, PA = NA, S = NA, SB = NA,
  H = NA, V = 3, a = NULL, q = NULL, Y = FALSE, j = FALSE,
  D = FALSE, St = Inf, Q = TRUE, constr = T, pholes = NA)

`mshape`	matrix: a kx2 matrix which is the reference matrix whose deformation is evaluated relatively to the shapes presented in "seqlist" argument. If links are provided the heatmap is computed in the constrained Delaunay triangulation defined by the links. Otherwise the Delaunay triangulation is not constrained.
`seqlist`	list: a list with 1 to 4 elements each containing a sequence of shapes that are contrasted with the reference shape. If more than one sequence is provided the sequences must contain the same number of shapes.
`suffix`	characther: suffix name to attch to the saved .png files (default = "anim")
`czlim`	logical: if more than one sequence is present in "seqlist" argument the zlim of all plot is common by default.
`czlimw`	logical: if TRUE and If more than one sequence is present in "seqlist" argument the zlim of all plot is different and common only within any specific sequence.
`linkss`	numeric: links for source configuration; if heat=T these (as well as "linkst" argument) must identify a closed contour in order to allow the Delaunay triangulation constrained within the external border.
`linkst`	numeric: links for target configuration
`colss`	numeric: landmarks color for source
`colst`	numeric: landmarks color for target
`lwds`	numeric: links width for source
`lwdt`	numeric: links width for target
`cexs`	numeric: cex parameter for landmarks of source
`cext`	numeric: cex parameter for landmarks of target
`displ`	logical: if TRUE displacement vectors are displayed
`axtit`	character: if NULL it uses as defaults: c("PC1+", "PC1-","PC2+", "PC2-","PC3+", "PC3-").
`mag`	numeric: magnification parameter for the illustrated deformation
`heat`	logical: if TRUE the heatmap is used. Heatmap is computed by calculating the log(determinant) of Jacobian matrix calculated using the first derivative of Thin Plate Spline function.
`mar`	numeric vector: "mar" argument in par()
`mai`	numeric vector: "mai" argument in par()
`oma`	numeric vector: "oma" argument in par()
`colors`	character: color palette for heatmap
`alpha`	numeric: transparency parameter for heatmpa color
`magrange`	numeric: zoom parameter for subplots. When this parameter is smaller the subplot is bigger.
`exts`	numeric vector: "ext" parameter in tpsgrid() function from "shapes" package
`PB`	numeric vector: "PB" argument from pslg() function in RTriangle package.
`PA`	matrix: "PA" argument from pslg() function in RTriangle package.
`S`	matrix: "S" argument from pslg() function in RTriangle package.
`SB`	numeric vector: "SB" argument from pslg() function in RTriangle package.
`H`	matrix: "H" argument from pslg() function in RTriangle package.
`V`	numeric: "V" argument from triangulate() function in RTriangle package.
`a`	numeric: "a" argument from triangulate() function in RTriangle package.
`q`	numeric: "q" argument from triangulate() function in RTriangle package.
`Y`	logical: "Y" argument from triangulate() function in RTriangle package.
`j`	logical: "j" argument from triangulate() function in RTriangle package.
`D`	logical: "D" argument from triangulate() function in RTriangle package.
`St`	numeric: "S" argument from triangulate() function in RTriangle package.
`Q`	logical: "Q" argument from triangulate() function in RTriangle package.
`constr`	logical: if TRUE a constrained triangulation according to links is performed
`pholes`	list: an optional list of vectors indicating points identifying holes in the input geometries

Paolo Piras

## Not run:  
### only one plot 
data(macrogroup)
data(my2d)
linksdors<-list(c(1,2),c(37,7),c(12,4),c(27,28),c(25,21),c(38,40),c(9,10),c(2,3),c(3,4),c(1,7),c(1,6),c(3,5),c(6,40),c(5,9),c(40,8),c(8,9),c(1,7),c(7,6),c(3,4),c(4,5),c(39,38),c(38,35),c(35,37),c(37,39),c(35,34),c(34,33),c(33,32),c(32,31),c(31,30),c(30,29),c(29,37),c(37,36),c(36,29),c(28,31),c(28,30),c(13,10),c(10,11),c(11,12),c(12,13),c(13,14),c(14,16),c(16,17),c(17,20),c(20,19),c(19,18),c(18,12),c(18,15),c(15,12),c(21,19),c(21,20),c(24,25),c(25,26),c(26,27),c(27,24),c(26,24),c(24,23),c(23,22),c(22,8),c(8,2))                                                                                                                                                           
amy2d<-procSym(my2d,CSinit=T,scale=F)
plot(amy2d$PCscores[,1:2],asp=1)
pc1seq<-list(scoresequencearray(amy2d$mshape,min(amy2d$PCscores[,1]),max(amy2d$PCscores[,1]),1,amy2d$PCs))
animdefo(amy2d$mshape,pc1seq,linkss=linksdors,linkst=linksdors)
#### multiplot with common zlim value
pc1seq<-scoresequencearray(amy2d$mshape,min(amy2d$PCscores[,1]),max(amy2d$PCscores[,1]),1,amy2d$PCs)
pc2seq<-scoresequencearray( amy2d$mshape,min( amy2d$PCscores[,2]),max( amy2d$PCscores[,2]),2, amy2d$PCs)
pc3seq<-scoresequencearray( amy2d$mshape,min( amy2d$PCscores[,3]),max( amy2d$PCscores[,3]),3, amy2d$PCs)
pc4seq<-scoresequencearray( amy2d$mshape,min( amy2d$PCscores[,4]),max( amy2d$PCscores[,4]),4, amy2d$PCs)
animdefo(amy2d$mshape,list(pc1seq,pc2seq,pc3seq,pc4seq),czlim=T,linkss=linksdors,linkst=linksdors)
#### plot for allometry indicating size values associated to shape change
##### Shape change associated to evolutionary allometry 
regr<-shaperegr(amy2d$orpdata,amy2d$size,links=linksdors,heatmap=T) ### 
myaxtits<-list(paste("Centroid Size=",round(regr$myseq,2)))###
#### 
animdefo(amy2d$mshape,list(regr$seqshapes),czlim=F,czlimw=T,a=0.01,linkss=linksdors,linkst=linksdors,axtit=myaxtits,magrange=1.5)

## End(Not run)