8.1. Alpha Diversity Analysis - DianaCarolinaVergara/16S-rRNA-Analysis GitHub Wiki

Alfa Diversity Analysis

Alpha diversity is the diversity in a single ecosystem or sample. The simplest measure is richness, the number of species (or OTUs, or ASVs) observed in the sample. Other metrics consider the abundances (frequencies) of the OTUs, for example to give lower weight to lower-abundance OTUs. The abundance distribution can be visualized using an octave plot (An octave plot (Edgar et al., 2018) is a histogram showing the OTU abundance distribution for a sample or a set of samples. This is a method for visualizing alpha diversity).

Interpretation

It is important to keep in mind that NGS amplicon sequencing can't reliably measure frequencies or presence / absence of OTUs, so the biological meaning of alpha diversity metrics developed for traditional ecology is unclear / misleading / difficult to interpret.

Estimators

Some rare species may not have been observed. An alpha diversity estimator attempts to extrapolate from the available observations (reads) to the total number of species in the community. The best-known estimator for NGS OTUs is Chao1. Another stimators are Shannon, Simpson, Margalef, etc.

Examples of alpha-diversity graphics

  1. Easy 001-graphics

  1. Advanced graphics in some papers:

Graphic of Alpha diversity and Constrained Analysis of Principal coordinates (CAP) plots for Penicillium communities in season, seaside, and substrate 1.

Non-phylogenetic ALFA metrics

Code:

To calculate an alpha-diversity analysis, in this case the -observed_otus metric.

We use the previously produced -table-dada2.qza result of the dada2 quality analysis, as a input file --i-table

Put the metric you want in --p-metric

qiime diversity alpha \
  --i-table table-dada2.qza \
  --p-metric observed_otus \
  --o-alpha-diversity observed_otus_vector.qza

Change --p-metric para chao1, simpson, shannon, margalef indexes.

Visually and statistically compare groups of alpha diversity values.

  • Parameters:

    --m-metadata-file The sample metadata. [required]

  • Outputs:

    --o-visualization The visualization file. [required]

  • Miscellaneous:

    --output-dir (PATH for the output files) Output unspecified results to a directory

    --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden).

    --citations Show citations and exit.

    --help Show this message and exit.

qiime diversity alpha-group-significance \
  --i-alpha-diversity core-metrics-results/faith_pd_vector.qza \
  --m-metadata-file sample_metadata.txt \
  --o-visualization core-metrics-results/faith-pd-group-significance.qzv

The previous one for faith-pd-vector and the next one for evenness-vector.

qiime diversity alpha-group-significance \
  --i-alpha-diversity core-metrics-results/evenness_vector.qza \
  --m-metadata-file sample_metadata.txt \
  --o-visualization core-metrics-results/evenness-group-significance.qzv