Code for analyses of immigrant microbiome project
- Set LIBDIR to full path of /lib directory
- Set working directory to the containing folder of this repo
- Then run:
- run.denovo.clr to plot figures using the de novo OTU-picking results with CLR transform
- run.denovo to plot figures using the de novo OTU-picking results
- run.shotgun to plot shotgun related figures only
- run.food to plot diet related figures
- load run.food after one of the previous 3 scripts to test for mb-diet associations
- run.Mouse to plot mouse related figures
- run.animation - makes longitudinal animation (has not been updated - might be broken)
- run.manuscript.figs - makes main and supplemental figures for manuscript