hidden
Aquafort eDNA
OTU Abundance
For this barplot, change the ‘level’ dropdown to ‘6’. Use the other drop down to sort the columns (samples) by date, stocked/not-stocked, ect. Click on the square on the taxonomy key to visualized only selected taxa. Interactive barplots of relative abundance can be found here
Core diversity metrics
PCoA is performed on distance matrices for the metrics below (seems to better handle missing data than PCA does). More complete descriptions here: https://docs.onecodex.com/en/articles/4150649-beta-diversity
- Alpha diversity
- Rarefaction
- Shannon’s diversity index (a quantitative measure of community richness)
- Faith’s Phylogenetic Diversity (a qualitative measure of community richness that incorporates phylogenetic relationships between the features)Kruskal-Wallis
- Observed OTUs (a qualitative measure of community richness) Kruskal-Wallis
- Beta diversity
- Jaccard distance (a qualitative measure of community dissimilarity. Qualitative - presence / absence - percentage of taxa not found in both samples) jaccard emperor
- Bray-Curtis distance (a quantitative measure of community dissimilarity. Takes into consideration abundance and presence absence) bray curtis emperor
- Unweighted UniFrac distance (a qualitative measure of community dissimilarity that incorporates phylogenetic relationships between the features. Percentage of phylogenetic branch length not found in both samples) unweighted unifrac emperor
- Weighted UniFrac distance (a quantitative measure of community dissimilarity that incorporates phylogenetic relationships between the features. Similar to Bray-Curtis but takes into consideration phylogenetic relationships) weighted unifrac emperor
Descriptons Coming Soon…
gemelli phylogenetic-rpca-with-taxonomy
Performs phylogenetic robust center log-ratio transform robust PCA and ranks the features by the loadings of the resulting SVD. One-way PERMANOVA: Determine whether groups of samples are significantly different from one another using a permutation-based statistical test. Tested here when grouping by pre- and post stocked, as well as tide. Test performed on the Aitchison distance of the sample loadings from RPCA.