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

Description Usage Arguments Author(s) Examples

This function displays in 2D the deformations associated typically to a procsym object from procSym() function in package "Morpho" (Stefan Schlager (2016). Morpho: Calculations and Visualisations Related to Geometric Morphometrics. R package version 2.4.1.1.https://github.com/zarquon42b/Morphor). However, the input list could contain any type of reference matrix, ordination scores and eigenvectors named "mshape" "PCscores" and "PCs" respectively.

plotdefo(procsymobject, zlim = NULL, linkss = NULL, linkst = NULL,
  colss = 1, colst = 2, lwds = 2, lwdt = 2, cexs = 0, cext = 0,
  displ = F, axtit = NULL, mag = 1, heat = T, mfrow = c(3, 2),
  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 = rep(0, 6), 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)

`procsymobject`	list: a list with three objects with the following names: "mshape" a kx2 matrix which is deformed according to the values and eigenvectors specified in the other two arguments; "PCscores" ordination scores coming from an ordination analysis; "PCs" eigenvectors relative to "mshape" and "PCscores". By default the function takes the first three PCscores columns and the first three PCs column to build the plot. The list can be built manually in order to contain the desired PCscores and PCs combination. If links are provided the heatmap is computed in the constrained Delaunay triangulation defined by the links. Otherwise the Delaunay triangulation is not constrained.
`zlim`	numeric: zlim range for heat (if TRUE) color.
`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.
`mfrow`	numeric vector: "mfrow" argument in par() tipically this default serves to display meaningfully positive and negative extremes of ordination scores
`mar`	numeric vector: "mar" argument in par()
`mai`	numeric vector: "mai" argument in par()
`oma`	numeric vector: "oma" argument in par()
`colors`	numeric: 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 geoemtries

Paolo Piras

## Not run:  
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$PCscores[,1:2],asp=1)
plotdefo(amy2d,linkss=linksdors,linkst=linksdors)
orbitR<-centroids(amy2d$mshape[c(18,19,20,17,16,14,13,12,15),])
orbitL<-centroids(amy2d$mshape[c(37,35,34,33,32,31,30,29,36),])
plotdefo(amy2d,linkss=linksdors,linkst=linksdors,H=rbind(orbitR,orbitL),pholes=list(c(18,19,20,17,16,14,13,12,15),c(37,35,34,33,32,31,30,29,36)))

## End(Not run)