An ordination has a limited set of uses. But are there alternatives to ordination for displaying beta-diversity data? In this episode, Pat shares one method for showing the change in microbial communities relative to a specific time or geographic point using R. He'll demonstrate this approach by using vegan, dplyr, and ggplot2.
You can find my blog post for this episode at https://www.riffomonas.org/code_club/2022-04-21-time-0-plot. The data were generated in our Kozich et al. 2013 paper (http://doi.org/10.1128/AEM.01043-13) using samples from the Schloss et al. 2012 paper (http://doi.org/10.4161/gmic.21008).
#ordination #microbiome #tidyverse #R #Rstudio #Rstats #ggplot2
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Microbial ecology data: https://www.riffomonas.org/minimalR/
General data: https://www.riffomonas.org/generalR/
0:00 An alternative to ordinations for visualizing community change
2:58 Filtering to get distance to day of weaning for each mouse
5:58 Generating raw version of figure
10:05 Cleaning up appearance of figure