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Fig. 5 | Genome Biology

Fig. 5

From: OncoNEM: inferring tumor evolution from single-cell sequencing data

Fig. 5

OncoNEM performance assessment. a Performance comparison of OncoNEM and five baseline methods. Shown are the distance and V-measure of inferred trees to ground truth. Results of single simulations are marked by dots and colored by method, while black horizontal bars indicate the mean over five simulations for each method. The distances shown were normalized for the number of cells n in the trees and were obtained by dividing the pairwise cell shortest-path distances by n(n−1)/2. Distances could only be calculated for three of the baseline methods. Values of the varied parameters are shown in the panels at the top. As default parameters, we used an FNR of 0.1, an FPR of 0.2, 200 sites, ten clones, no unobserved clones, 20 cells and 20 % missing values. b Performance comparison of OncoNEM and Kim and Simon’s oncogenetic tree method. Shown is the mutation order accuracy of the inferred trees for each of the simulated data sets. This measure is undefined for data sets without mutually exclusive mutations. Therefore, no values are shown for the single-clone case and the first replicate of the five-clone scenario, for which the simulated tree is linear

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