3.1. Interactive results panels
The results interface presents the user with graphical representations of computation results via maps, bubble plots, krona charts (Ondov et al., 2011), phylogeny trees, alpha and beta-diversity plots, nMDS ordinations and barcharts (Figure 2). The results are organized by sample on graphs (except for the overall krona chart), and sample contextual information is displayed on mouse hover over the coloured circles on the maps and bubble plots. The results are stored and remain available via the web page URL for 15 days after job submission.
3.1.1.Community ecological analysis results
The maps representing OTU geographic distribution presented as a result of a “Community ecological analysis ” query are computed using three distinct metrics: i) relative abundance, ii) Shannon diversity index and iii) richness (number of OTUs) for each sample depths (Figure 2A). Abundance is calculated as barcode counts divided by the sum of counts for the corresponding sample. Richness is computed from rarefied barcode counts. Relative abundance, Shannon diversity index or richness comparisons are possible between distinct plankton size fractions and/or sampling depths using distinct world maps.
Co-variation of barcodes abundance and environmental variables can be examined on bubble plots (Figure 2B) for selected combinations of sampling depths and plankton size fractions. A scatter plot is drawn if the user selects the option “Abundance/environmental variables ” (Figure 2C).
The taxonomic distributions of the target barcodes are displayed in multi-layered and interactive krona charts for each distinct sample (by clicking on the circles in the world map; Figure 2A) and for the full dataset (Figure 2E).
The beta-diversity of the selected taxon using either Bray-Curtis dissimilarity or Jaccard distance is represented by nMDS ordinations with optional projections of the 3 selected variable vectors using the R vegan package envfit function (Figure 2F). A glossary of available environmental variables - both measured in situ and estimated from modelling - is provided to help users select variables of interest. Dot colors and shapes on the graphs are related to sample depths and plankton size fractions.
Alpha-diversity is represented by two box- or scatter plots (Figure 2G). The first plot represents the richness (OTU number) according to a user selected environmental variable, whilst the second represents the Shannon diversity index.
Finally, relative abundance and richness of rDNA metabarcodes are represented on bar charts for the 9 most abundant taxonomy groups depending on sample depths and plankton size fractions (Figure 2H).