Relative Abundance and Community Similiarity of Conditionally Rare Taxa

Quick Start

• Open crt_taraoceans.Rmd
• Click "knit"
• crt.rds contains the output from the CRT function and can be loaded in case of time or memory constraints.

Example Output

Summary

What is the visualization?

• This is an non-metric multidimensional scaling (NMDS) plot used to visualize the relationship between communities based on a chosen distance metric (i.e., Bray-Curtis, Unifrac, etc.).
• DCM = Deep Chlorophyll Maximum Layer; MES = Mesopelagic Zone; MIX = Marine Epipelagic Mixed Layer; SRF = Surface Water Layer

What data goes in (and what preprocessing is necessary)?

• Visualization requires otu table, taxonomy table, and metadata for creating a phyloseq object. Output "OTUdf_cr_excel.txt" requires user to open file in excel to delete first row, first column, then the contents of the first cell. The amended file is saved as "OTUdf_cr_input.txt" and used for the CRT function.

How should we use/interpret this visualization?

• Visualization can be used to compare the similarity of communities that include all taxa and conditionally rare taxa.
• Depth is responsible for 35% and 19% of the variance observed in community composition of all taxa and conditionally rare taxa, respectively
• Province is responsible for 13% and 15% of the variance observed in community composition of all taxa and conditionally rare taxa, respectively.
• Depth may not be as important as other factors in structuring the microbial communities of conditionally rare taxa.

Authors

• Alexandria Igwe
• github id: anigwe
• ORCID:0000-0001-5993-1203

Links

Zenodo Binder, doi: LINK_TO_BINDER

Github Binder:

Github Repository: https://github.com/speeding-up-science-workshops/ord_abund_raretaxa