Supplementary Figure 3: Measures for selecting optimal signature number.

A comparison of signature number (x axis) across four measures for determining optimal signature number. The circle and solid lines represent the results from the BriTROC-1 samples run, whereas the triangles and dotted lines represent results from 1,000 randomly permuted BriTROC-1 matrices (these can be considered a null measure). Here basis refers to the signature-by-component matrix, coefficients refers to the patient-by-signature matrix, and consensus refers to the connectivity matrix of patients clustered by their dominant signature across 1,000 runs. The best fit is the run that showed the lowest objective score across the 1,000 runs. A value of 7 defines the point of stability in the cophenetic, dispersion and silhouette coefficients and is the maximum sparsity achievable above the null model for the basis matrix.