NMDS can be done in the vegan library using the metaMDS function - see help file for details of plotting etc. There is a heatmap function in the default stats library for use with dendrograms. Copy one of the examples and substitute your data.

Data import depends on how your data are formatted, just about anything can be read from csv files to sql databases.

Thank you

I found Sebastian Rashka (he's on ResearchGate) his book on heat maps on R really helped as well as this online tutorial

http://www.molecularecologist.com/2013/08/making-heatmaps-with-r-for-microbiome-analysis/

Then I tackled each error as they happened, it helps if you make yourself familiar with the command line language and once you know what you want R to do it's pretty straight forward.

Hope this helps,

Ciara