Fig. 1
From: Variant effect predictions capture some aspects of deep mutational scanning experiments
DMS experiments vs. variant effect predictions. In a hexbin plot, 17,781 deleterious effect SAVs in SetCommon were compared to normalized scores for three prediction methods (SNAP2 [38], Envision [49], and Naïve Conservation). Values on both axes range from 0 (neutral) to 1 (maximal effect) as denoted by the gradient from white (neutral) to red (effect). Dashed red lines give linear least-squared regressions. Marginals denote distributions of experimental and predicted scores with a kernel density estimation overlaid in blue. The footer denotes Spearman ρ, Pearson R and the mean squared error together with the respective 95% confidence intervals. The method scores are given on the y-axes and reveal the method: a SNAP2, b Envision – the only method trained on DMS data, c Naïve Conservation read off PSI-BLAST profiles