Report summary
Perform analysis of time series datasets (taken from the same subjects at different time).
| Created | 27/11/2019 |
|---|---|
| Updated | 12/04/2020 |
| Type | Time series report |
| Project | NIIOR ACI CCI exploratory |
| Uploaded samples | 46 |
Metadata
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Taxonomic composition
Heatmap of taxonomic composition
The interactive heatmap represents relative abundance of major microbial taxa (columns) in the samples (rows). Using the drop-down list “Heatmap settings” on the right of the heatmap, users can select taxonomic rank of interest. For convenience of comparison between close values, clicking on a cell “freezes” the displayed value of cell on the Legend and additionally the displayed abundance of top 10 taxa of corresponding sample (click again or on the cross near sample name to “unfreeze”). Use the Top control to change the way of major composition display between the top features in the selected sample and the top features across all samples on the average.
Analysis of outliers
Automatic filtering of the user samples with extreme taxonomic composition (based on the combined analysis of user and external data). Analysis of outliers: samples in upper 1% tail of distribution of median distance between each sample and closest 50% of neighbours approximated by normal distribution. List of outliers:
No outliers detected.
PCoA visualization based on taxonomic composition
Distribution of the samples by their taxonomic composition in reduced dimensionality. The closer the samples (points) on the plot, the more similar their composition. Vectors show the directions in which the levels of the respective major taxa increase. Method of dimension reduction: PCoA (Principal Coordinate Analysis); dissimilarity metric: weighted UniFrac. Clicking on a dot “freezes” the detailed information about the sample on the right of the plot (click again or on the cross near sample name to “unfreeze”). Switch between the display modes with or without outliers and with or without vectors showing major microbial “drivers” using the respective controls.
Alpha-diversity
The measure describes the conditional number of taxa in each sample. Metric: Shannon index. Clicking on a dot “freezes” the displayed value on Y axis and additionally the abundance of top 10 taxa (click on it or on the cross near the sample name to “unfreeze”). In addition, the mean and confidence interval value appear when the mouse is over the boxplot. Controls at the top and bottom-right allow to change the displayed data.
Stability tests results
Stability is treated in sense of presence of unit-root in time series. 100 most abundant bacterial OTU from each subject are considered as independent serie and unit root tests (ADF and KPSS) are performed upon these OTUs. Plot shows logarithms of p-values for each OTU across these 2 tests. Green lines represent p-value threshold of 1%.
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Phylogenetics analysis of stability
In analysis section results of stability module are implemented in order to test if unstable OTUs are taxonomically close. In plot section taxonomic tree is shown(based on GreenGenes OTU tree). Inner circle corresponds to OTUs phyloums, outer circle -- to stability state
Analysis
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Taxonomic table
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datalab:
3.10.0
knb_interactive:
2.0.2
knb_lib:
4.8.50