You might want to try the visNetwork package, which is based on htmlwidgets. The documentation says:
compatible with shiny, R Markdown documents, and RStudio viewer
I've used visNetwork to build a flowchart and then talk through it with people using the RStudio Viewer (but I've never tried it with R Markdown), where they can point and click to add nodes and edges, which sounds similar to what you want to do? I think it is a really useful package, hopefully it is what you need!