About graph-like content in Rmarkdown, you have also UML diagrams and the new nomnoml which as a knit engine included.
It is not DOT I think but in case someone coming to this post is interesting to UML, it could be useful.
BTW, If your question's been answered, would you mind choosing a solution? It helps other people see which questions still need help, or find solutions if they have similar problems. Here’s how to do it: