morphomap2Dmap {morphomap}

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)
}