data-Physeq: The physeq data was modified from the (Data) Global patterns...

In guokai8/microbial: Do 16s Data Analysis and Generate Figures

The physeq data was modified from the (Data) Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample (2011)

Description

Published in PNAS in early 2011. This work compared the microbial communities from 25 environmental samples and three known “mock communities” – a total of 9 sample types – at a depth averaging 3.1 million reads per sample. Authors were able to reproduce diversity patterns seen in many other published studies, while also invesitigating technical issues/bias by applying the same techniques to simulated microbial communities of known

References

Caporaso, J. G., et al. (2011). Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. PNAS, 108, 4516-4522. PMCID: PMC3063599

Examples

data(Physeq)
plot_richness(physeq, x="SampleType", measures=c("Observed", "Shannon"))

guokai8/microbial documentation built on July 23, 2024, 4:14 a.m.