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).