morphomapDF: morphomapDF

In morphomap: Morphometric Maps, Bone Landmarking and Cross Sectional Geometry

morphomapDF

Description

Tool to build a data.frame suitable for morphometric maps

Usage

morphomapDF(
  morphomap.thickness,
  rem.out = TRUE,
  fac.out = 0.5,
  smooth = TRUE,
  scale = TRUE,
  smooth.iter = 5,
  method = "equiangular",
  unwrap = "A"
)

Arguments

morphomap.thickness	list: morphomap.Thickness object
rem.out	logical: if TRUE the outlier will be removed
fac.out	numeric: parameter to set the threshold in outliers detection
smooth	logical: if TRUE the smooth algorithm is applied
scale	logical: if TRUE the thichkness matrix is scaled from 0 to 1
smooth.iter	numeric: number of smoothing iterations
method	character: if set on "equiangular" the cortical 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 cortical thickness is calculated at each point as the closest distance between external and internal outlines
unwrap	character: starting qaudrant to unwrap the diaphysis ("A"=anterior, "L"=lateral, "P"=posterior, "M"=mesial)

Value

XYZ data.frame for morphometric map

labels character vector for x labels in the morphometric map

Author(s)

Antonio Profico, Luca Bondioli, Pasquale Raia, Paul O'Higgins, Damiano Marchi

Examples

library(lattice)
library(colorRamps)
data(HomFem38023)
meshes<-morphomapSegm(HomFem38023, param1=4)
perMesh<-meshes$external
endMesh<-meshes$internal
mech_length<-380.23
rawSections<-morphomapCore(out.sur=perMesh,
                           inn.sur=endMesh,num.sect=61,mech.len = mech_length, 
                           start = 0.2,end=0.8)
shapeSections<-morphomapShape(rawSections,21,sects_vector=NULL,cent.out="CCA",delta=0.1)
femthick<-morphomapThickness(shapeSections)
dataDF<-morphomapDF(femthick)$XYZ
contourplot(dataDF[, 3] ~ dataDF[, 1] + dataDF[, 2],
            col.regions=blue2green2red(101),region=TRUE,
            colorkey=list(at=seq(0,1,length.out = 100)),
            scales = list(x = list(at = seq(0,100,length.out = 5), c("A","M","P","L","A"), 
            alternating = 1)),asp=1.5,cuts=20,xlab="femur margin",ylab="biomechanical length")

morphomap documentation built on Oct. 10, 2023, 1:08 a.m.