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Mouse Biogeography

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