::: {.cell layout-align="center" hash='03-dge-pretty_cache/html/newplot_8d6e4f987983b570b1a35d7e158d7540'}

```{.r .cell-code}
# Prepare the data for plotting
res_df <- as.data.frame(deseq2.res)
res_df$gene <- row.names(res_df)
# Create volcano plot
volcano_plot <- ggplot(res_df, aes(x = log2FoldChange, y = -log10(padj), color = padj < 0.05)) +
  geom_point(alpha = 0.6, size = 1.5) +
  scale_color_manual(values = c("grey", "red")) +
  labs(title = "Volcano Plot",
       x = "Log2 Fold Change",
       y = "-Log10 Adjusted P-value",
       color = "Significantly\nDifferentially Expressed") +
  theme_minimal() +
  theme(panel.grid.major = element_blank(),
        panel.grid.minor = element_blank(),
        legend.position = "top")
print(volcano_plot)
```

::: {.cell-output .cell-output-stderr}
```
Warning: Removed 41435 rows containing missing values (`geom_point()`).
```
:::

::: {.cell-output-display}
![](03-dge-pretty_files/figure-html/newplot-1.png){fig-align='center' width=576}
:::
:::