It can be shown that for a positive semi-definite matrix C the distance matrix D with elements obtained by the standard transformation  is Euclidean and B is a centered inner product matrix ([19], pp. 402). Therefore principal components can be obtained from (partial) eigenvalue decomposition of B. Thus, for 2D-visualization we compute the two leading eigenvectors x1 and x2 of B associated with the largest and second largest eigenvalue, respectively. The M components of x1 and x2 provide the x1 and x2 coordinates for the M genes, which are utilized for scatter plot visualization.