Partial Correlation with Clinical Variables and metabolites

Hi there, I am conducting a secondary analysis on a small dataset in the metadata analysis section. I have metabolites and clinical data (Plasma concentrations, age, weight, etc). My question is if I have two time points pre and post drug use how does the correlation analysis consider the time points? When it gives results it give graphs and on the graphs it gives correlations for both time points? If they have taken a medication between the two is this a confounding element and how do I account for that?