Creating a Heatmap with ggplots2

Another problem I see is that the Abundance column is of the type character. You can fix that

mine.long$Abundance <- as.numeric(mine.long$Abundance)

However, I do not expect that to fix the error message. Can you make a reproducible example from a subset of your data? It would be enough to have two categories of and two of Metabolite. Then post the data and the call to ggplot. Others can then work with exactly the data you are using. Information about how to make a reproducible example are in the following post: