processing metagenomics data in R

I have metagenomics data for a set of samples and I need to generate heatmaps and perform principle component analysis on these datasets and I need some help developing my code in R—I have draft code that I am working from but I need some assistance configuring my tables so that I can apply the analysis. I have some experience in R but haven't worked in it in quite a long time and need to refamiliarize myself with vectors, objects, etc. as pertain to large sample sets.