TL;DR If you are getting crappy looking png images from rmarkdown html or word documents, try using type=‘cairo’ or dev=‘CairoPNG’ in your chunk options.
PNG Graphics?? So, I write a lot of reports using rmarkdown and knitr, and have been using knitr for quite a while. My job involves doing analyses for collaborators and communicating results. Most of the time, I will generate a pdf report, and I get beautiful graphics, thanks to the eps graphics device.
TL;DR Currently available methods to discover metal geometries make too many assumptions. We were able to discover novel zinc coordination geometries using a less-biased method that makes fewer assumptions. These novel geometries seem to also have specific functionality. This work was recently published under an #openaccess license in Proteins Journal: Yao, S., Flight, R. M., Rouchka, E. C. and Moseley, H. N. B. (2015), A less-biased analysis of metalloproteins reveals novel zinc coordination geometries.