text: user285: This paper Fig2b
  
  b Changes of chromatin accessibility in AMD (n = 14) relative to
  normal (n = 11) in all retina samples. Each dot represents one
  ATAC-Seq peak. Blue line in the left panel indicates average fold
  changes of peaks with the same ATAC-Seq intensity. The percentage of
  reduced peaks is shown under the density curve in the right panel.
  
  How is the density calculated or what is being shown there? average ATAC seq signal or Fold change?
  
  user5077: They are not referring to density of reads. It is the density of the fold change, the y variable in the plot to left of Fig2b. It tells you the distribution of the foldchange and 92% of the fold change is <0.
  See this page for more details on density and histograms
  Suppose your data is something like this (purely making this up):
  set.seed(555)
  fc = rnorm(1000,-0.5,2)
  averATAC = -0.5*(fc - 0.5)^2 + 0.2*fc + 3  + rnorm(100,25,10)
  
  You fit a density to it and you get the plot:
  par(mfrow=c(1,2))
  plot(averATAC,fc)
  plot(dens$y,dens$x,xlab = "density",ylab="fc")
  
  
  
original_text: 285: <p>This paper <a href="https://www.nature.com/articles/s41467-018-03856-y/figures/2" rel="nofollow noreferrer">Fig2b</a></p>
  <blockquote>
  <p>b Changes of chromatin accessibility in AMD (n = 14) relative to
  normal (n = 11) in all retina samples. Each dot represents one
  ATAC-Seq peak. Blue line in the left panel indicates average fold
  changes of peaks with the same ATAC-Seq intensity. <strong>The percentage of
  reduced peaks is shown under the density curve in the right panel.</strong></p>
  </blockquote>
  <p>How is the density calculated or what is being shown there? average ATAC seq signal or Fold change?</p>
   5077: <p>They are not referring to density of reads. It is the density of the fold change, the y variable in the plot to left of Fig2b. It tells you the distribution of the foldchange and 92% of the fold change is &lt;0.</p>
  <p>See <a href="https://www.statmethods.net/graphs/density.html" rel="nofollow noreferrer">this page for more details on density and histograms</a></p>
  <p>Suppose your data is something like this (purely making this up):</p>
  <pre><code>set.seed(555)
  fc = rnorm(1000,-0.5,2)
  averATAC = -0.5*(fc - 0.5)^2 + 0.2*fc + 3  + rnorm(100,25,10)
  </code></pre>
  <p>You fit a density to it and you get the plot:</p>
  <pre><code>par(mfrow=c(1,2))
  plot(averATAC,fc)
  plot(dens<span class="math-container">$y,dens$</span>x,xlab = &quot;density&quot;,ylab=&quot;fc&quot;)
  </code></pre>
  <p><a href="https://i.stack.imgur.com/VYK9s.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/VYK9s.png" alt="enter image description here" /></a></p>
  