morphomapDF {morphomap}

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")