``` r
# Plot all replicate R2s, with features sorted by mean R²
ggplot(all_MP_highperf, aes(x = Feature, y = R2)) +
  geom_point(aes(color = as.factor(Replicate)), size = 1.5) +
  geom_point(aes(y = Mean_R2), color = "black", shape = 18, size = 3) + 
  geom_hline(yintercept = mean(all_MP_highperf$R2, na.rm = TRUE),
             linetype = "dashed", color = "blue") +
  theme_minimal() +
  labs(title = "Model Performance Across Gene Expression",
       x = "Gene Expression Feature (Ordered by Mean R²)",
       y = "R² (Variance Explained)",
       color = "Replicate") +
  theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
  ylim(0, 1)
```

```
## Warning: Removed 2 rows containing missing values or values outside the scale range
## (`geom_point()`).
```

![](22.3-Apul-multiomic-machine-learning-byTP_files/figure-gfm/unnamed-chunk-69-1.png)<!-- -->