Please find the code used to create the manuscript. The code has been separated by the tool used to generate figures. The code utilizes import tools from QIIME2 objects and proceeds to analyze the object as a phyloseq object and a data frame. There are portions that the object and metadata map remains as a data frame and as a phyloseq object. Please follow the code comments.

Please contact Dr. Qingsheng.Li@nyulangone.org for further clarification or questions.