Fig. 3

Results on two semi-simulated datasets (AML-sim and BCR-XL-sim). a TPR vs. FDR of methods on AML-sim under three scenarios (weak, medium, and strong) when trees have 400, 900, and 1600 leaves (see Additional file 1: Table S3 for a tabular format of plot a). Methods are in colors. FDR cutoffs are at 0.01, 0.05, and 0.1. b DA branches identified by methods in the medium scenario of AML-sim using a tree with 900 leaves. The four panels show the tree, truth, observations, and results. The tree panel displays non-DA branches (without AML blast cells) in dashed lines to save space, colors branches with AML blast cells above 50% in purple, and labels nodes identified by methods; the truth panel shows cell type compositions and cell counts (point sizes) of leaves; the observation panel shows cell counts on leaves (rows) in samples (columns) split by groups; the result panel annotates leaves identified by methods. c same as a, except the BCR-XL-sim dataset is presented. d same as b, except the medium scenario of BCR-XL-sim using 400-leaf tree is presented. Here, only one feature (pS6) is shown