Introduction
The Taxonomy tree
contains taxonomy profiling of two groups of samples with the phylogenetic taxonomy tree from kingdom to species. The background color of tree branches represents different taxonomy. The highlight branches color in red and blue represents the taxonomies significantly different between provided two groups. The outer names are species names, and the significant different species have rectangles around their names. The nodes of the tree reveal the average abundance of the corresponding taxonomy among all samples.
Input Files
Click on the Download Data
button to check the demo input files.
1. Profiling table (TSV file)
- header
samples ID - row names
Taxonomy names in mpa format. Should have a complete record from kingdom to species. (MetaPhlAn3 default output is acceptable)
2. Differential testing result (TSV file)
- header
ID | mean(case) | sd(case) | mean-rank(case) | occ-rate(case) | mean(control) | sd(control) | mean-rank(control) | occ-rate(control) | enriched | pvalue | qvalue |
---|---|---|---|---|---|---|---|---|---|---|---|
k__Bacteria | 97.10 | 10.41 | 60 | 1.00 | 99.39 | 2.98 | 70 | 1.00 | control | 0.14 | 0.49 |
- rows
Every taxonomy mentioned in profiling tables should have a row with the name of a minimal taxonomy level. (e.g.k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia
should had a rowg__Akkermansia
in this file) The analysis module differential testing could output the required format.
3. Group information (TSV file)
- header
ID | Group |
---|---|
sample1 | case |
- rows
sample ID and the group information for the corresponding sample.
Display Interactions
- Tooltips
Hover on the tree node and a info tooltip of node name, group, and p-value will show. - Download Chart
One SVG file will be generated when theDownload Chart
button is clicked. - Download Data
The compressed files inzip
will be downloaded when theDownload Data
button is clicked.
Sidebar Functions
Files
- Manage Files: checklist of files uploaded previously, delete or download files.
- Upload: upload files. Note that the duplicated file name will be alerted and given a random postfix.
- Choose: choose files uploaded previously.
Settings
- Classification Rank: tree will be colored by the classifications of the selected rank.
- Leaves Level: tree will to the selected rank.
- Name Display: select the display of the leaves name from three options below:
- Show All Name: show all leaves name.
- Highlight Distinct Name: show all leaves name and highlight distinct leaves with border.
- Show No Name: do not show the leaves name.
- Show Distinct Nodes Only: check the checkbox to draw distinct nodes only.
- Q-value: input a threshold Q-value, the input should be between 0 and 0.5.