Fig. 2. Association between prognosis and either cell type fraction or cell state of nonmalignant cells in three TCGA tumor types.
a, Violin plots showing distribution of cell type fraction in each tumor type. Median fractions are denoted by white dots and upper/lower quartiles by bars. Oligo., oligodendrocytes. b,c, Kaplan–Meier plots showing survival associations with infiltration of T cells (b) and macrophages (c) in SKCM. Δmedian, median survival time in the high group/median survival time in the low group. d, Scatter plot showing correlation between BayesPrism expression estimates in macrophages and M1 and M2 macrophage subtype scores across three tumor types. Boxes mark the 25th percentile (bottom), median (central bar) and 75th percentile (top); whiskers represent extreme values within 1.5-fold of interquartile range. Statistical significance was determined by one-way analysis of variance (P < numeric limit and degrees of freedom = 2 for both M1 and M2 scores; M1, F = 203.44; M2, F = 63.226), followed by reporting of Tukey’s honestly significant difference-adjusted P values. n(GBM) = 127, n(HNSCC) = 26 and n(SKCM) = 225 independent TCGA bulk tumor samples. e, Kaplan–Meier plots showing survival associations with the M1/M2 polarization state of macrophages in SKCM. b,c,e, P values were derived from log-rank test, HR was defined by high/low and 95th percentile confidence intervals are shown in square brackets. Transparent colors denote 95% confidence bands.