<p>Dear all,</p>

<p>I am trying to find a R package to plot LD blocks.</p>

<p>I found LDheatmap package but I would prefer a graphical representation as in haploview with LD blocks, and options to add lines or select markers on the graph.</p>

<p>Thank you for your help.</p>

<p>Steven</p>

<p>If you are particular about an R package, I would like to suggest <a href='http://cran.r-project.org/web/packages/snp.plotter/'>snp.plotter package</a>. See snp.plotter reference manual <a href='http://cran.r-project.org/web/packages/snp.plotter/snp.plotter.pdf'>here</a>. </p>

<p>Example plot from snp.plotter:</p>

<p><img src='http://bioinformatics.oxfordjournals.org/content/23/6/774/F1.medium.gif' alt='alt text' /> </p>

<p>In addition, I would like to suggest <a href='http://csg.sph.umich.edu/locuszoom/'>LocusZoom</a> or <a href='http://www.broadinstitute.org/mpg/snap/'>SNAP</a> for visualization of LD blocks.  </p>

<p>There is a <a href='https://statgen.sph.umich.edu/locuszoom/genform.php?type=yourdata'>web-interface</a> and standalone <a href='http://genome.sph.umich.edu/wiki/LocusZoom_Standalone'>package</a> available for LocusZoom. </p>

<p>Example figure using LocusZoom: </p>

<p><img src='http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2935401/bin/btq419f1.jpg' alt='alt text' /></p>

<p>Example figure using SNAP: </p>

<p><img src='http://bioinformatics.oxfordjournals.org/content/24/24/2938/F1.medium.gif' alt='alt text' /></p>

<p>Manuscript describing snp.plotter <a href='http://www.ncbi.nlm.nih.gov/pubmed/17234637'>here</a>, LocusZoom <a href='http://www.ncbi.nlm.nih.gov/pubmed/20634204'>here</a> and SNAP <a href='http://bioinformatics.oxfordjournals.org/content/24/24/2938.full'>here</a>.   </p>
