text: user14269: I'd like to run dotPlotly from RStudio but I can't find any description/help for this. Is it at all possible?
  Another side to this question: does anyone know any tool for dot plots for genome comparison apart from pafr (doesn't provide colour legend) and d-genies (we have problems with installation)? Is there a way to make dot plots for a minimap2 output with ggplot2?
  To specify:
  
  I need help in running dotPlotly (preferably from Rstudio)
  I'd like to build dot plots for genome comparisons showing % of identity
  
  Thanks
  
  user2108: For the issue of just making a dotplot in ggplot2 from a PAF file, it is pretty trivial to do a simple one, though it is necessarily not the most beautiful.
  I grabbed 2 random E. coli genomes and mapped them:
  % minimap2 ~/Downloads/GCF_000157115.2_Escherichia_sp_3_2_53FAA_V2_genomic.fna.gz ~/Downloads/GCF_000308975.1_ASM30897v2_genomic.fna.gz > 2_ecolis.paf
  
  Then I opened Rstudio and ran the following (which is only slightly modified from what I was first shown by an old colleague, Zev Kronenberg):
  ecoli_paf = read.table("~/2_ecolis.paf", sep="\t", fill=T)
  ggplot() + 
  geom_segment(
    data=ecoli_paf, mapping=aes(
      x=ecoli_paf$V3, y=ecoli_paf$V8, xend=ecoli_paf$V4, yend=ecoli_paf$V9, color=ecoli_paf$V6
    )
  )
  
  I am far from a ggplot2 expert as you can tell, and there are a few issues here (reverse complement is shown opposite to what you'd expect, linear interpolation of mappings from mapped endpoints), but it makes a somewhat informative dotplot:
  
  I am confident that with minimal fiddling you can make this look a lot better. I will try to revisit and beautify.
  
original_text: 14269: <p>I'd like to run dotPlotly from RStudio but I can't find any description/help for this. Is it at all possible?
  Another side to this question: does anyone know any tool for dot plots for genome comparison apart from pafr (doesn't provide colour legend) and d-genies (we have problems with installation)? Is there a way to make dot plots for a minimap2 output with ggplot2?</p>
  <p>To specify:</p>
  <ol>
  <li>I need help in running dotPlotly (preferably from Rstudio)</li>
  <li>I'd like to build dot plots for genome comparisons showing % of identity</li>
  </ol>
  <p>Thanks</p>
   2108: <p>For the issue of just making a dotplot in ggplot2 from a PAF file, it is pretty trivial to do a simple one, though it is necessarily not the most beautiful.</p>
  <p>I grabbed 2 random E. coli genomes and mapped them:</p>
  <pre><code>% minimap2 ~/Downloads/GCF_000157115.2_Escherichia_sp_3_2_53FAA_V2_genomic.fna.gz ~/Downloads/GCF_000308975.1_ASM30897v2_genomic.fna.gz &gt; 2_ecolis.paf
  </code></pre>
  <p>Then I opened Rstudio and ran the following (which is only slightly modified from what I was first shown by an old colleague, Zev Kronenberg):</p>
  <pre><code>ecoli_paf = read.table(&quot;~/2_ecolis.paf&quot;, sep=&quot;\t&quot;, fill=T)
  ggplot() + 
  geom_segment(
    data=ecoli_paf, mapping=aes(
      x=ecoli_paf$V3, y=ecoli_paf$V8, xend=ecoli_paf$V4, yend=ecoli_paf$V9, color=ecoli_paf$V6
    )
  )
  </code></pre>
  <p>I am far from a ggplot2 expert as you can tell, and there are a few issues here (reverse complement is shown opposite to what you'd expect, linear interpolation of mappings from mapped endpoints), but it makes a somewhat informative dotplot:</p>
  <p><a href="https://i.stack.imgur.com/h7WCR.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/h7WCR.png" alt="enter image description here" /></a></p>
  <p>I am confident that with minimal fiddling you can make this look a lot better. I will try to revisit and beautify.</p>
  