morphomap (version 1.5)

morphomapPlotShape: morphomapPlotShape

Description

Visualize 2D and 3D cross sections

Usage

morphomapPlotShape(
  Shape,
  dims = 3,
  col1 = "red",
  col2 = "green",
  colc = "orange",
  colr = "violet",
  coll1 = "darkred",
  coll2 = "darkgreen",
  size = 1.5,
  lwd = 0.7,
  colmesh1 = "red",
  colmesh2 = "green",
  alpha = 0.3,
  tri = TRUE,
  outlines = TRUE,
  points = TRUE,
  lines = FALSE,
  centroid = FALSE,
  cent.out = "CCA",
  delta = 0.1,
  vecs = NULL
)

Arguments

Shape

list: output from morphomapShape function

dims

numeric: 2 = bi-dimensional cross sections, 3 = three-dimensional cross sections

col1

color of the external outline

col2

color of the internal outline

colc

color of the centroid of the cross section

colr

color of the radii

coll1

color of the lines on the enternal outline

coll2

color of the lines on the internal outline

size

numeric: points and spheres size

lwd

numeric: line width in pixels

colmesh1

color of the periosteal mesh

colmesh2

color of the endosteal mesh

alpha

numeric: alpha value between 0(fully transparent) and 1 (opaque)

tri

logical: if TRUE the semilandmarks configuration is triangulated

outlines

logical: if TRUE the 2D and 3D outlines are plotted

points

logical: if TRUE points (2D) and spheres (3D) are plotted

lines

logical: if TRUE 2D and 3D lines are plotted

centroid

logical: if TRUE 2D and 3D centroids are plotted

cent.out

how to define the center of each section. The method allowed are "CCA" (center of cortical area), "E" (barycenter of the external outline) and "I" (barycenter of the internal outline)

delta

pixel size used to calculate the CCA

vecs

numeric: which sections will be plotted. If dims is set on 2 only the first element of the vector vecs is considered

Author

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

Examples

if(interactive()){
#morphomap on a human femur bone
data(HomFem38023)
meshes<-morphomapSegm(HomFem38023)
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, side="left")
#Plot the object morphomapShape in three dimensions
morphomapPlotShape(shapeSections,dims=3, size=0.5)
#Plot a 2D cross-section 
morphomapPlotShape(shapeSections,dims=2,lines=TRUE,vecs=31)
}