Fix cutoff ordering in make_phy_df()

[JCSzamosi]

I think this will screw things up for group-mean taxa barcharts when the cutoff is >0 because the non-zero total will be removed from the denominator. Need to make sure I understand exactly what this is doing.

# Set all counts < the cutoff to zero
phyloseq::otu_table(phyl_glommed)[phyloseq::otu_table(phyl_glommed) <
                                      cutoff] = 0