map.to.interval: Map points from MDS final configuration to interval starting at 0.

Description

Maps points from the final configuration of a 2-dimensional spherically constrained wMDS to an interval with a starting point at 0.

Usage

map.to.interval(mdsobject, nloci)

Value

A list with the elements:

chromlength: A named vector giving the position of each marker.
order: A named vector giving the rank order of the markers.
locilength: A named vector giving the position of each marker in order of increasing distance along the segment.
maporder: A named vector of the position in the input list of each marker in order of increasing distance along the segment.

Arguments

mdsobject: The output from smacofSphere.
nloci: The number of markers in the configuration.

Details

Centres the configuration on zero and calculates the median distance of the points from the origin. Finds the largest gap in the spherical configuration and assigns the marker on the right hand side of it angle 0. Converts Cartesian coordinates to polar coordinates and projects points onto the arc centred on 0 with radius the median distance from the origin.

Examples

Run this code

# M and lod should be n x n symmetric matrices of the same dimensions where
# n is the number markers to be analysed
if (FALSE) {
mds1<-smacofSphere(M,ndim=2,algorithm=dual,weightmat=lod,penalty=100)
pol<-map.to.interval (m1,n)
}