text: user1075: I have a data frame containing 4 columns:
  
  Chrom: chromosome name of the feature
  Start: starting base of the feature 
  End: end base of the feature
  Name: name of the feature, e.g. 5S ribosomal RNA
  
  The head of the data frame is shown below:
        Chrom    Start      End                        Name
      1     1 15390242 15390720 16S ribosomal RNA (partial)
      2     1 15390900 15391794 16S ribosomal RNA (partial)
      3     1 15392798 15396046           23S ribosomal RNA
      4     1 15397439 15397917 16S ribosomal RNA (partial)
      5     1 15398097 15398991 16S ribosomal RNA (partial)
      6     1 15399995 15403243           23S ribosomal RNA
  
  I want to plot these features on the karyotype of C. elegans. I am using the chromPlot package from Bioconductor.
  I am using the following code:
  
  Subsetting the original data frame to get a data frame for each feature type: 5S, 16S and 23S rRNAs
  annot1 <- dplyr::filter(cel, Name == '5S ribosomal RNA')
  annot2 <- dplyr::filter(cel, Name == '23S ribosomal RNA')
  annot3 <- dplyr::filter(cel, Name == '16S ribosomal RNA (partial)')
  
  and then plot:
  chromPlot(gaps = cel, figCols = 2, annot1 = annot1, annot2 = annot2)
  
  
  This is OK because the two features are far away in the genome. However, if I try:
  chromPlot(gaps = cel_gap, figCols = 2, annot1 = annot1, annot2 = annot2,
            annot3 = annot3)
  
  
  one of the features masks the other because they are close to each other in the genome. How can I make the green bar stack on top of the yellow one instead of covering it?
  
  user1075: chromPlot(gaps = cel_gap, figCols = 2, annot1 = annot1, annot2 = annot3, annot3 = annot2,
            chrSide=c(1, 1, -1, 1, -1, 1, -1, 1))
  
  The chrSide argument decides on which side the histogram goes, so it can be used to solve my problem. The bars are not stacked but the result is the same: more accurate visualisation. 
  Thanks to Llopis for the guidance.
  
  
original_text: 1075: <p>I have a data frame containing 4 columns:</p>
  
  <ul>
  <li>Chrom: chromosome name of the feature</li>
  <li>Start: starting base of the feature </li>
  <li>End: end base of the feature</li>
  <li>Name: name of the feature, e.g. 5S ribosomal RNA</li>
  </ul>
  
  <p>The head of the data frame is shown below:</p>
  
  <pre><code>      Chrom    Start      End                        Name
      1     1 15390242 15390720 16S ribosomal RNA (partial)
      2     1 15390900 15391794 16S ribosomal RNA (partial)
      3     1 15392798 15396046           23S ribosomal RNA
      4     1 15397439 15397917 16S ribosomal RNA (partial)
      5     1 15398097 15398991 16S ribosomal RNA (partial)
      6     1 15399995 15403243           23S ribosomal RNA
  </code></pre>
  
  <p>I want to plot these features on the karyotype of <em>C. elegans</em>. I am using the <a href="https://bioconductor.org/packages/devel/bioc/vignettes/chromPlot/inst/doc/chromPlot.pdf" rel="nofollow noreferrer">chromPlot</a> package from Bioconductor.</p>
  
  <p>I am using the following code:</p>
  
  <ul>
  <li><p>Subsetting the original data frame to get a data frame for each feature type: 5S, 16S and 23S rRNAs</p>
  
  <pre><code>annot1 &lt;- dplyr::filter(cel, Name == '5S ribosomal RNA')
  annot2 &lt;- dplyr::filter(cel, Name == '23S ribosomal RNA')
  annot3 &lt;- dplyr::filter(cel, Name == '16S ribosomal RNA (partial)')
  </code></pre>
  
  <p>and then plot:</p>
  
  <p>chromPlot(gaps = cel, figCols = 2, annot1 = annot1, annot2 = annot2)</p></li>
  </ul>
  
  <p><a href="https://i.stack.imgur.com/4HnwQ.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/4HnwQ.png" alt="Karyotype with 2 annotations"></a></p>
  
  <p>This is OK because the two features are far away in the genome. However, if I try:</p>
  
  <pre><code>chromPlot(gaps = cel_gap, figCols = 2, annot1 = annot1, annot2 = annot2,
            annot3 = annot3)
  </code></pre>
  
  <p><a href="https://i.stack.imgur.com/hWrx3.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/hWrx3.png" alt="Karyotype with 3 annotations"></a></p>
  
  <p>one of the features masks the other because they are close to each other in the genome. How can I make the green bar stack on top of the yellow one instead of covering it?</p>
   1075: <pre><code>chromPlot(gaps = cel_gap, figCols = 2, annot1 = annot1, annot2 = annot3, annot3 = annot2,
            chrSide=c(1, 1, -1, 1, -1, 1, -1, 1))
  </code></pre>
  
  <p>The <code>chrSide</code> argument decides on which side the histogram goes, so it can be used to solve my problem. The bars are not stacked but the result is the same: more accurate visualisation. </p>
  
  <p>Thanks to Llopis for the guidance.</p>
  
  <p><a href="https://i.stack.imgur.com/VkMv9.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/VkMv9.png" alt="karyotype"></a></p>
  