<p>Please let me know any tools or R packages that can create a mutation diagram showing mutations in protein domains like this figure from the MSKCC cBio Cancer Genomic Portal? Thanks in advance <br />
<img src='http://www.cbioportal.org/public-portal/images/previews/tp53_mutations.png' alt='enter image description here' /></p>

Pfam provides an online tool to not only generate the domain information in JSON format, but to draw the lollipop diagram using javascript as well. They have more information [here][1].

IMHO, not as pretty as cBioPortal's but it gets you close to a solution.

**EDIT / SHAMELESS PLUG**: After seeing the data available and how easy it'd be, I made my own quick tool to fetch the data and draw the diagram for me in a style similar to cBioPortal - feel free to fork it and add features: https://github.com/pbnjay/lollipops

Example output (w/ labels per the comments)

<img alt="TP53 w/ 2 mutations" src="http://i.imgur.com/ave33Cn.png" style="height:58px; width:600px" />

 [1]: http://pfam.xfam.org/help#tabview=tab9