Taxonomic visualizations¶
This page explains the main taxonomic visualization outputs generated by MTD Explorer.
These outputs help users inspect taxonomic structure after Kraken2 classification and Bracken abundance estimation.
The two main visualization tools are:
- KronaTools, for interactive taxonomic exploration;
- GraPhlAn, for publication-style cladogram visualizations.
Where these outputs are stored¶
Taxonomic visualization outputs are usually stored in:
A typical output directory may contain:
krona/
├── SAMPLE-bracken.html
├── SAMPLE-bracken.krona
├── all_animals-bracken.html
└── all_animals-bracken.krona
graphlan/
├── Combined.mpa
├── Combined_for_graphlan.mpa
├── graphlan_input.clean.tsv
├── tree.txt
├── annot.txt
├── outtree.txt
├── outimg.png
├── outimg.pdf
├── outimg.cladogram_species_top80.png
└── outimg.cladogram_species_top80.pdf
Exact filenames may vary depending on the selected taxonomic rank, sample names, and plotting settings.
Krona interactive visualization¶
MTD Explorer uses KronaTools to generate interactive HTML visualizations of taxonomic profiles.
The main combined file is usually:
A documentation example is available here:
Open example Krona visualization in a new page
Tip
The embedded viewer is interactive. Click inside the Krona plot to zoom into taxonomic levels.
For a larger view, open the example in a new page using the link above.
What Krona shows¶
KronaTools displays taxonomy as an interactive radial hierarchy.
Users can click through taxonomic levels to inspect broad and narrow taxonomic assignments.
This is useful for exploring:
- dominant high-level taxonomic groups;
- taxa nested under broader clades;
- unexpected classifications;
- sample-level or combined taxonomic profiles.
How to interpret Krona¶
The center of the plot represents broad taxonomic levels.
Outer layers represent more specific taxonomic assignments.
Larger segments represent larger taxonomic contributions in the profile used to build the plot.
Because the plot is interactive, users can zoom into a clade and inspect its substructure.
What not to conclude from Krona alone¶
Do not treat a large Krona segment as proof of infection, contamination, or biological association.
Do not interpret a taxonomic assignment without considering database design, read support, sample metadata, and Kraken2 reports.
Do not compare samples only by visual impression when formal comparison or normalization is required.
Krona is best used as an exploratory navigation tool.
GraPhlAn cladogram¶
MTD Explorer uses GraPhlAn to generate cladogram-style visualizations of detected taxa.
Output location¶
GraPhlAn outputs are stored in:
The main image files are usually:
Compatibility output names may also be present:
What the GraPhlAn plot shows¶
The GraPhlAn cladogram summarizes detected taxa in a hierarchical taxonomic tree.
The center represents broader taxonomic levels.
Outer rings represent more specific taxonomic levels.
Highlighted labels or markers indicate selected taxa included in the displayed tree.
In MTD Explorer, the default cladogram is designed to show a readable subset of detected species, such as the top detected taxa.
How to interpret the cladogram¶
Use the cladogram to inspect taxonomic structure.
It can help answer questions such as:
This plot is especially useful for visually summarizing complex taxonomic profiles.
What not to conclude from the cladogram alone¶
Do not interpret visual prominence as statistical significance.
Do not assume that a taxon is biologically important only because it appears in the displayed tree.
Do not treat the absence of a taxon from the figure as absence from the dataset, because the figure may show only a selected subset of taxa.
For interpretation, check the Bracken abundance tables, Kraken2 reports, ranked detected-microbiome tables, and methods parameters.
Krona vs GraPhlAn¶
KronaTools and GraPhlAn are complementary.
| Output | Best for |
|---|---|
| Krona HTML | Interactive exploration of taxonomic hierarchy |
| GraPhlAn PNG/PDF | Static summary figure for reports, slides, and manuscripts |
Use KronaTools when you want to explore taxonomic levels interactively.
Use GraPhlAn when you need a static visual summary of the detected taxonomic structure.
Files to inspect first¶
For taxonomic visualization outputs, start with:
krona/all_animals-bracken.html
graphlan/outimg.cladogram_species_top80.png
graphlan/outimg.cladogram_species_top80.pdf
graphlan/Combined.mpa
graphlan/graphlan_input.clean.tsv
methods/mtd_methods_run_parameters.csv
The methods/mtd_methods_run_parameters.csv file is useful because it records
the database paths, taxonomic settings, Kraken2 parameters,
Bracken parameters, and software versions.
When outputs may be missing¶
Taxonomic visualization outputs may be absent when:
- no microbiome taxa were detected;
- the Bracken abundance table is missing;
- the taxonomic table is empty after filtering;
- KronaTools or GraPhlAn failed;
- a visualization step failed but the pipeline continued with a warning;
- output generation was skipped because required intermediate files were absent.
Check the pipeline log and the corresponding output folders for details.
Next step¶
After reviewing taxonomic visualizations, return to Output files or continue to the Command-line reference.