-
Notifications
You must be signed in to change notification settings - Fork 2
7. Graphical user interface
The GUI's main header prominently displays the project title and houses essential controls such as the live update toggle and the shut down button. The timestamp for the most recent update appears beneath the live update toggle.
When live updates are enabled, the GUI periodically fetches new data generated by the backend pipeline from the Nanopore batch files. This update frequency is configurable in the settings file. Note that enabling live updates will reset any zoom levels or modifications made to the Sunburst chart and Sankey plot. However, certain settings like selected domains, taxonomic levels, and read cutoffs will be retained. Pausing live updates allows for uninterrupted exploration of the plots.
You can capture snapshots of graphs using icons located at the top-right corner of each graph area. Zoom functionality is also available via these icons. Additionally, you can zoom in or out within the entire application using Ctrl + mouse wheel, just like any standard web page.
To assist with navigation, INFO/HELP buttons and tooltips are strategically positioned throughout the GUI. These provide contextual explanations for various functions and elements, including the live update toggle and the validation checkbox.
Pressing the Shut Down Program button will trigger a prompt, enabling users to terminate backend processes. Note that you must close the browser window manually to fully exit the program.
The GUI layout is organized into four distinct tabs:
-
Most Abundant Hits: This section lists the taxa with the highest read counts in the sample.
-
Species of Interest: This displays a color-coded list and bar chart featuring the specified species of interest. Species exceeding a preset read count threshold (defaulted to 100) will appear in red.
This tab offers a detailed account of quality control metrics. It shows:
- The time-series of processed reads and base pairs.
- Batch-wise read and base pair counts.
- Cumulative statistics, including total processed reads, excluded reads with reasons, successfully classified reads, and the number of processed batch files.
The Sankey plot in Nanometa Live functions as an intuitive visualization tool resembling a phylogenetic tree. It's designed to offer users a clear overview of the lineage and relationships of the most abundant taxa present in a sample. This plot visually maps the flow and transitions between different taxonomic levels, making it easier to understand the hierarchical structure and relative abundance of various taxa. It is particularly useful for quickly identifying major lineages and understanding their proportional representation in the sample.
The Sunburst chart offers a comprehensive and interactive way to explore the taxonomic data. At its core, the root node represents the base of the taxonomic hierarchy, with lineages branching out towards the outer rim of the chart. This radial layout allows for an immediate grasp of the hierarchical structure and diversity within the sample. Each concentric ring in the chart corresponds to a different taxonomic level, providing a detailed and scalable view of the data. The Sunburst chart is particularly effective for exploring the finer details of the taxonomic distribution and for comparing the relative abundances of taxa at multiple levels.