text: user285: So I'm doing a pathway analysis using GeneTrail database. One thing I am not able to get is this similarity measure being calculated and plotted: 
  
  I want to know how this is being made, what is the output being plotted because each gene is may be involved in multiple pathways.
  I want to be able to make it in R again. Any suggestion or help would be appreciated. How to plot the enrichment result in this form ?
  
  user48: This is a a symmetric matrix with the pathways in both axes. So for each pair a similarity index is calculated (usually it takes into account the number of genes in each pathway and the total number of genes in both pathways). There are several similarity indexes available. A typical one is Jaccard or Sørensen-Dice index, usually 0 means no similarity and 1 equal pathways.
  You can do this kind of analysis in R using BioCor (Disclosure: I am the author of this package) which uses the Dice similarity. You will need the name of the genes of each pathway, after calculating the similarity of pathways using mpathSim, you can then plot it with a heatmap (using the heatmap function).
  
original_text: 285: <p>So I'm doing a pathway analysis using <a href="https://genetrail2.bioinf.uni-sb.de/start.html" rel="nofollow noreferrer">GeneTrail</a> database. One thing I am not able to get is this similarity measure being calculated and plotted: </p>
  
  <p><a href="https://i.stack.imgur.com/cG2f7.jpg" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/cG2f7.jpg" alt="figure"></a></p>
  
  <p>I want to know how this is being made, what is the output being plotted because each gene is may be involved in multiple pathways.</p>
  
  <p>I want to be able to make it in R again. Any suggestion or help would be appreciated. How to plot the enrichment result in this form ?</p>
   48: <p>This is a a symmetric matrix with the pathways in both axes. So for each pair a similarity index is calculated (usually it takes into account the number of genes in each pathway and the total number of genes in both pathways). There are several similarity indexes available. A typical one is <a href="https://en.wikipedia.org/wiki/Jaccard_index" rel="nofollow noreferrer">Jaccard</a> or <a href="https://en.wikipedia.org/wiki/S%C3%B8rensen%E2%80%93Dice_coefficient" rel="nofollow noreferrer">Sørensen-Dice</a> index, usually 0 means no similarity and 1 equal pathways.</p>
  
  <p>You can do this kind of analysis in R using <a href="https://bioconductor.org/packages/BioCor/" rel="nofollow noreferrer">BioCor</a> (Disclosure: I am the author of this package) which uses the Dice similarity. You will need the name of the genes of each pathway, after calculating the similarity of pathways using <code>mpathSim</code>, you can then plot it with a heatmap (using the <code>heatmap</code> function).</p>
  