This vignette runs the code to make the plots from the following paper:
Dick JM, Kang X. 2023. chem16S: community-level chemical metrics for exploring genomic adaptation to environments. Bioinformatics 39(9): btad564. doi: 10.1093/bioinformatics/btad564
This vignette was compiled on 2024-03-11 with JMDplots 1.2.19-11 and chem16S 1.0.0-16.
## [1] "map_taxa: mapping rate to GTDB taxonomy is 100.0%"
## [1] "map_taxa: using these manual mapping(s) to NCBI RefSeq:"
## [1] "map_taxa: can't map groups order_Stramenopiles (12.94%), family_ACK-M1 (3.27%), 374 others (11.75%)"
## [1] "map_taxa: mapping rate to RefSeq taxonomy is 71.9%"
Data sources: The GlobalPatterns
dataset is from the phyloseq package (McMurdie and Holmes, 2013) and is adapted from Caporaso et al. (2011). The mouse gut dataset was created by analyzing sequence data from Schloss et al. (2012) (downloaded here and used in the mothur MiSeq SOP and DADA2 Pipeline Tutorial) with the DADA2 pipeline modified to use the GTDB training set (Alishum, 2022) for taxonomic classifications.
Alishum A. 2022. DADA2 formatted 16S rRNA gene sequences for both bacteria & archaea. Zenodo. doi: 10.5281/zenodo.6655692
Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Lozupone CA, Turnbaugh PJ, Fierer N, Knight R. 2011. Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proceedings of the National Academy of Sciences 108(Supplement 1): 4516–4522. doi: 10.1073/pnas.1000080107
McMurdie PJ, Holmes S. 2013. phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data. PLOS One 8(4): e61217. doi: 10.1371/journal.pone.0061217
Schloss PD, Schubert AM, Zackular JP, Iverson KD, Young VB, Petrosino JF. 2012. Stabilization of the murine gut microbiome following weaning. Gut Microbes 3(4): 383–393. doi: 10.4161/gmic.21008