EnhancedVolcano underrepresenting DEGs

Question

[jabbari.parnian]

I'm plotting my DEGs from DESeq2 with EnhancedVolcano, but I can see that not all genes that have LFC > 1 or < -1 are shown in the plot. The number of red dots on the plot is clearly lower than the number of genes. Does anyone know what might be the reason?

[ATpoint]

results %>%
  ggplot(aes(x=log2FoldChange, y=-log10(padj))) +
  geom_point()

Use that to inspect your data, everything else is eye-candy. Confirm with this that you're seeing what you expect.