Thank You for your suggestions.
I did exactly as you said. First added abundance value in mapping file for that particular OTU and plotted make_emperior.oy by passsing --add_unique_columns and --color_by that OTU abundance. and it worked fine for me.
My another question related to this is: What is I want to do exactly the same (color samples by abundance value of particular OTU) for creating 2d PCoA, because emperior creates 3d PCoA only. Is there any way I can do it here or in R?
Thank you again for your quick solution