Supplementary Figure 8: Comparison of cell assignment between five methods on experimental data across 32 fibroblast lines.

(a) The fraction of assignable cells (i.e., highest P > thresholds) when varying the thresholds from 0.5 to 0.95. Shown are box plots depicting median and the first and third quantiles of the 32 lines. (b) The adjusted Rand index of cell assignment to clones between the five considered methods. The values are averaged across 32 fibroblast lines. (c) Scatter plot between the uncertainty of the inferred tree from cardelino-free (x-axis) and the mean absolute difference of the assignment probability between cardelino-free and cardelino (y-axis). The output posterior clonal configuration matrix from cardelino-free consists of the probability of each variant being present in each clone. A completely uninformative clonal tree would have all entries equal to 0.5. Thus, we measure the uncertainty of the output tree from cardelino-free by taking 0.5 minus the mean absolute difference of the posterior probability configuration matrix and the uninformative configuration probability matrix of all of entries equal to 0.5. With this measure, a value of 0.5 indicates a posterior configuration indistinguishable from the uninformative configuration and a value of 0 indicates very high-confidence from the model in the posterior configuration. (d) The comparison of cell assignment for one representative line (feec) when using different guide clonal trees sampled from Canopy’s posterior distribution as input. Each violin plot shows the adjusted Rand index of cell assignment between each of 435 tree pairs combining the 30 most probable trees from bulk exome-seq for the feec line. (e) Cell assignment similarity for each of the 32 lines when using different guide clonal trees, quantified with adjusted Rand index values between different pairs of guide clonal trees. For each line, we take the 30 most probable posterior trees from Canopy, and then each dot in the box plot denotes the average adjusted Rand index value for one line, calculated from 435 of these pairwise comparisons.