::: {.cell layout-align="center" hash='03-dge-pretty_cache/html/unnamed-chunk-18_9948d3f939e43831383613371700ce97'}

```{.r .cell-code}
tmp <- deseq2.res
# The main plot
plot(tmp$baseMean, tmp$log2FoldChange, pch=20, cex=0.45, ylim=c(-3, 3), log="x", col="darkgray",
     main="DEG Dessication  (pval <= 0.05)",
     xlab="mean of normalized counts",
     ylab="Log2 Fold Change")
```

::: {.cell-output .cell-output-stderr}
```
Warning in xy.coords(x, y, xlabel, ylabel, log): 16484 x values <= 0 omitted
from logarithmic plot
```
:::

```{.r .cell-code}
# Getting the significant points and plotting them again so they're a different color
tmp.sig <- deseq2.res[!is.na(deseq2.res$padj) & deseq2.res$padj <= 0.05, ]
points(tmp.sig$baseMean, tmp.sig$log2FoldChange, pch=20, cex=0.45, col="red")
# 2 FC lines
abline(h=c(-1,1), col="blue")
```

::: {.cell-output-display}
![](03-dge-pretty_files/figure-html/unnamed-chunk-18-1.png){fig-align='center' width=576}
:::
:::