morphomapPlotShape: morphomapPlotShape

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

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(s)

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)
}

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