text: user2005: I am trying to make MA-plot for my bulk-RNA-seq dataset and experiencing issues with it. I just copy-pasted the code that can be found here:
  https://f1000research.com/articles/4-1070/v2
  which is:
  library("DESeq2")
  plotMA(resLFC1, ylim=c(-5,5))
  topGene <- rownames(resLFC1)[which.min(resLFC1$padj)]
  with(resLFC1[topGene, ], {
    points(baseMean, log2FoldChange, col="dodgerblue", cex=2, lwd=2)
    text(baseMean, log2FoldChange, topGene, pos=2, col="dodgerblue")
  })
  
  However, I am not getting the right plot with the top gene circled, but the following one:
  
  Maybe it is a bug in the plotMA function, not sure. How can I reproduce the figure from the publication?
  
  user77: It's likely that the fold-change of the topGene is greater than 5. Consequently, the circle is being drawn and the text produced, but they're outside the bounds of the plot (the bounds don't update if you add a circle and text label). Look at the log2FoldChange column of resLFC1[topGene, ] and increase the bounds to encompass that.
  
original_text: 2005: <p>I am trying to make <code>MA</code>-plot for my <code>bulk-RNA-seq</code> dataset and experiencing issues with it. I just copy-pasted the code that can be found here:</p>
  
  <p><a href="https://f1000research.com/articles/4-1070/v2" rel="noreferrer">https://f1000research.com/articles/4-1070/v2</a></p>
  
  <p>which is:</p>
  
  <pre><code>library("DESeq2")
  plotMA(resLFC1, ylim=c(-5,5))
  topGene &lt;- rownames(resLFC1)[which.min(resLFC1$padj)]
  with(resLFC1[topGene, ], {
    points(baseMean, log2FoldChange, col="dodgerblue", cex=2, lwd=2)
    text(baseMean, log2FoldChange, topGene, pos=2, col="dodgerblue")
  })
  </code></pre>
  
  <p>However, I am not getting the right plot with the top gene circled, but the following one:</p>
  
  <p><a href="https://i.stack.imgur.com/SwZ1R.png" rel="noreferrer"><img src="https://i.stack.imgur.com/SwZ1R.png" alt="enter image description here"></a></p>
  
  <p>Maybe it is a bug in the <code>plotMA</code> function, not sure. How can I reproduce the figure from the publication?</p>
   77: <p>It's likely that the fold-change of the <code>topGene</code> is greater than 5. Consequently, the circle is being drawn and the text produced, but they're outside the bounds of the plot (the bounds don't update if you add a circle and text label). Look at the <code>log2FoldChange</code> column of <code>resLFC1[topGene, ]</code> and increase the bounds to encompass that.</p>
  