<p>The plot is from <a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3575466/pdf/cc-12-379.pdf">this publication, see page 2</a> the bottom of the plot with ACTG letters in different colours and sizes.</p>

<ol>
	<li>Could anyone clarify in layman&#39;s terms what it represents?</li>
	<li>More importantly, how do we plot it using R or any other tools?</li>
</ol>

<p>Here is the plot, if you can&#39;t access the paper:</p>

<p><img alt="" src="https://dl.dropboxusercontent.com/u/32553873/StackOverflow/Dennisplot.PNG" style="height:198px; width:390px" /></p>

<p>Found related post at SO: <a href="http://stackoverflow.com/questions/5438474/plotting-a-sequence-logo-using-ggplot2">Plotting a &ldquo;sequence logo&rdquo; using ggplot2?</a></p>

<p>The plot shows the comparison of the reference human sequence with N-number of samples (patients). The samples turn to have variation of sequences in that region. Now from these samples, you can compare the probability how often a given nucleotide is mismatched/mutated in sapmles. If the letter is big it means the sequence is invariant.</p>

<p>You can use weblogo either in their webpage or in R to make that figure.</p>

<p>Or if you have Chip-seq peaks, you can do motif analysis and make those plots using HOMER tools.</p>
