morphomap2Dmap: morphomap2Dmap

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

morphomap2Dmap

Description

Create a 2D cortical thickness map

Usage

morphomap2Dmap(
  morphomap.shape,
  rem.out = FALSE,
  fac.out = 0.5,
  smooth = FALSE,
  scale = TRUE,
  smooth.iter = 5,
  gamMap = FALSE,
  nrow = 90,
  ncol = 100,
  gdl = 250,
  method = "equiangular",
  unwrap = "A",
  plot = TRUE,
  pal = blue2green2red(101),
  aspect = 2
)

Arguments

morphomap.shape	list: output from morphomapShape function
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 a smooth 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
ncol	numeric: number of columns for gam smoothing
gdl	numeric: number of degree of freedom for gam smoothing
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)
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

Value

dataframe dataframe for colormap production

2Dmap thickness color map

gamoutput output from GAM

data input used to build the GAM map

Author(s)

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

Examples

if (interactive()){
library(colorRamps)
#morphomap on a human femur bone
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,24,sects_vector=NULL,cent.out="CCA",
delta=0.1, side="left")

#built 2D morphometric map without GAM smoothing
bone2Dmap<-morphomap2Dmap(morphomap.shape=shapeSections,
                          plot = TRUE, rem.out = TRUE,fac.out = 1.0, pal = blue2green2red(101),
                          aspect=2)
#built 2D morphometric map with GAM smoothing
bone2Dmap<-morphomap2Dmap(morphomap.shape=shapeSections,gam=TRUE,
                          plot = TRUE, rem.out = TRUE,fac.out = 1.0, pal = blue2green2red(101),
                          aspect=2)

#morphomap on a chimpanzee femur bone
data(PanFem27713)
meshes<-morphomapSegm(PanFem27713, param1=3)
perMesh<-meshes$external
endMesh<-meshes$internal
mech_length<-277.13
rawSections<-morphomapCore(out.sur=perMesh,
                           inn.sur=endMesh,num.sect=61,mech.len = mech_length, start = 0.2,end=0.8)
shapeSections<-morphomapShape(rawSections,24,sects_vector=NULL,cent.out="CCA",
delta=0.1, side="left")
#built 2D morphometric map without GAM smoothing
bone2Dmap<-morphomap2Dmap(morphomap.shape=shapeSections,plot = TRUE, 
rem.out = TRUE,fac.out = 1.0,pal = blue2green2red(101),aspect=2)
#built 2D morphometric map with GAM smoothing
bone2Dmap<-morphomap2Dmap(morphomap.shape=shapeSections,gam=TRUE,
                          plot = TRUE, rem.out = TRUE,fac.out = 1.0,pal = blue2green2red(101),
                          aspect=2)
}

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