Scripts used in "Biogeographical distribution of gut microbiome composition and function is only partially recapitulated by fecal transplantation into germ-free mice".

This repository concerns reproducing the figures found in the manuscript.

Raw data can be found in the NCBI database: http://www.ncbi.nlm.nih.gov/bioproject/944800.

Repository layout:

• CS_SPF : Cedars-Sinai SPF dataset files
• Donors_Analysis : HUM MD Gavage dataset files
• Humanized-Biogeography-Analysis : HUM SD Gavage and SPF Gavage dataset files
• Regional-Mouse-Biogeography-Analysis : UCLA O. SPF Dataset files
• Shotgun : shotgun metagenomics for 4 datsets
• UCLA_V_SPF_Analysis : UCLA V. SPF dataset files
• melonnpan_model : Trained model used for predicting metabolites from KO microbiome data
• Miscellaneous files
  • Are utilized in the figures scripts

To clone this repository:

git clone https://github.com/julianneyang/biogeography

To reproduce the figures in this repository:

• Navigate to MouseBiogeography-RProj/Final_Figures and run each script to produce the corresponding figure.
  • Note that filepaths are built to the top level of the repo.
  • Each of the following scripts corresponds to the main figures:
    • Figure 2: Figure_2_Taxa_Barplots_Aggregated.R
    • Figure 3: Figure_3_Luminal_Alpha_Beta_Diversity.R
    • Figure 4: Figure_4_Genus_Site_Heatmaps_Clustering.R
      • Note that the final versions of these heatmaps can be found in Figure_4_Heatmaps as cosmetic changes were made in Inkscape or Adobe Illustrator
    • Figure 6: Figure_6_GMM_Coef_Plots.R
    • Figure 7: Figure_7_GBM_Coef_Plots.R
• All other supplementary figures can be reproduced in the same manner