morphomapDF | R Documentation |
Tool to build a data.frame suitable for morphometric maps
morphomapDF( morphomap.thickness, rem.out = TRUE, fac.out = 0.5, smooth = TRUE, scale = TRUE, smooth.iter = 5, method = "equiangular", unwrap = "A" )
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) |
XYZ data.frame for morphometric map
labels character vector for x labels in the morphometric map
Antonio Profico, Luca Bondioli, Pasquale Raia, Paul O'Higgins, Damiano Marchi
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")
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