Toothnroll (version 1.11)

Tooth2Dmap: Tooth2Dmap

Description

Create 2D morphometric maps of enamel/dentin thickness

Usage

Tooth2Dmap(
  tooth.shape,
  input,
  rem.out = FALSE,
  fac.out = 0.5,
  smooth = FALSE,
  scale = TRUE,
  smooth.iter = 5,
  gamMap = FALSE,
  nrow = 120,
  ncol = 80,
  gdl = 250,
  method = "equiangular",
  plot = TRUE,
  pal = blue2green2red(101),
  aspect = 0.6,
  labels = c("Li", "Mes", "Bu", "D", "Li"),
  ylab = ""
)

Value

dataframe dataframe for colormap production

2Dmap thickness color map

gamoutput output from GAM

data input used to build the GAM map

Arguments

tooth.shape

list: output from the function ToothShape

input

list: output from the function ToothAlignment

rem.out

logical: if TRUE outliers will be removed

fac.out

numeric: parameter to set the threshold in outlier detection

smooth

logical: if TRUE a smoothing filter is applied

scale

logical: if TRUE the thichkness matrix is scaled from 0 to 1

smooth.iter

numeric: number of smoothing iterations

gamMap

logical: if TRUE gam smoothing is applied

nrow

numeric: number of rows for gam smoothing matrix

ncol

numeric: number of columns for gam smoothing matrix

gdl

numeric: number of degree of freedom for gam smoothing matrix

method

character: if set on "equiangular" the dentine or enamel thickness is meant as the distance of the segment intersecting the external and internal outline starting from the centroid of the section. If set on "closest" the dentine or enamel thickness is calculated at each point as the closest distance between external and internal outlines

plot

logical: if TRUE the 2D morphometric map is plotted

pal

character vector: colors to be used in the map production

aspect

numeric: axis ratio for 2D morphometric map

labels

character vector: names for x labels in the morphometric map

ylab

character vector: label for y axis in the morphometric map

Author

Antonio Profico; Mathilde Augoyard

Examples

# \donttest{
data("URI1_tooth")
require(morphomap)
Enamel<-URI1_tooth$mesh1
Dentin<-URI1_tooth$mesh2
Pulp<-URI1_tooth$mesh3
outline<-URI1_tooth$outline
set<-URI1_tooth$set
#Map of the crown
AlignMeshes<-ToothAlignment(mesh1=Enamel,mesh2=Dentin,mesh3=Pulp,set,outline,analyse = "c")
#Virtual sectioning dentine-pulp
External<-AlignMeshes$almesh1$mesh
Internal<-AlignMeshes$almesh2$mesh
#Define 16 cross-sections from the 30% to the 90% along the crown
Core<-ToothCore(External,Internal,num.points = 1000,num.sect =16,
                    bio.len = AlignMeshes$length,start=0.3,end=0.9)
#Extract 25 equiangular semilandmarks from each cross-section (anticlockwise)
Shape<-ToothShape(Core,25,sects_vector = NULL,cent.out = "E",direction="a")
Tooth2Dmap(Shape,AlignMeshes,rem.out =TRUE,scale=FALSE,smooth = FALSE,aspect = 0.5,gamMap = FALSE,
           nrow = 100,ncol = 100,gdl = 250,method="equiangular")

#Map of the root
AlignMeshes<-ToothAlignment(mesh1=Enamel,mesh2=Dentin,mesh3=Pulp,set,outline,analyse = "r")
#Virtual sectioning dentine-pulp
External<-AlignMeshes$almesh2$mesh
Internal<-AlignMeshes$almesh3$mesh
#Define 16 cross-sections from the 10% to the 50% along the root
Core<-ToothCore(External,Internal,num.points = 1000,num.sect =16,
                    bio.len = AlignMeshes$length,start=0.1,end=0.5)
#Extract 25 equiangular semilandmarks from each cross-section (anticlockwise)
Shape<-ToothShape(Core,25,sects_vector = NULL,cent.out = "E",direction="a")
Tooth2Dmap(Shape,AlignMeshes,rem.out =FALSE,scale=FALSE,smooth = FALSE,aspect = 0.5,gamMap = FALSE,
           nrow = 100,ncol = 100,gdl = 250,method="equiangular")
# }