Talk:Chromosome structure via Euclidean Distance Matrices

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%%% Ronan Fleming, E.coli molecule data

%%% -Jon Dattorro, August 2008

clear all

load ecoli

frame = 12; % 1 through 12

G = her49imfs12movfull(frame).cdata; % uint8

G = (double(G)-128)/128; % Gram matrix

N = size(G,1);

D = diag(G)*ones(N,1)' + ones(N,1)*diag(G)' - 2*G; % EDM D

clear her49imfs12movfull G;

Vn = [-ones(1,N-1); speye(N-1)];

VDV = (-Vn'*D*Vn)/2;

clear D Vn

[evec evals flag] = eigs(VDV, [], 20, 'LR');

if flag, disp('convergence problem'), return, end;

close all

Xs = sqrt(real(evals(1:3,1:3)))*real(evec(:,1:3))'; % Projection of -VDV on PSD cone rank 3

plot3(Xs(1,:), Xs(2,:), Xs(3,:), '.')

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