I am analyzing a nontargeted metabolomic data set using ComplexHeatmap. After I made a heatmap of all identified metabolites, I decided to continue the analyses only of compounds that are in one cluster. How do I extract the data from e.g. Cluster1 and make a new dataframe out of it?

I'm not familiar with ComplexHeatmap, but if it produces a tree (as resulting from hclust e.g.) you can directly pass it to cutree().