Viewing the MaAsLin3 Results

By navigating to the "Comparative Analysis" menu, you'll be able to view your generated MaAsLin3 comparatives. The comparative analysis will contain data in 7+ different tabs (as described below).

MaAsLin2 Results

Input Data

A pre-formatted .tsv table containing taxonomic or functional profiling results (values dependent on input parameters).

Input Metadata

A pre-formatted .tsv table containing all sample metadata.

Association Results

Perhaps the most important output from MaAsLin 2 is the list of significant associations displayed in the Association Results, which displays significant associations between metadata and microbial features along with effect size, p-values, and q-values.

The full list of associations that pass MaAsLin 2's significance threshold is ordered by increasing q-values. Columns are:

• Feature Name: the microbial feature (taxon, gene, pathway, etc.).
• Metadata: the variable name being associated with a microbial feature.
• Value Name: for categorical features, the specific feature level for which the coefficient and significance of association is being reported.
• Coefficient/EffectSize + Standard Error: fit coefficient and standard error from the model.
  • In abundance models, a one-unit change in the metadatum variable corresponds to a
    2^coef fold change in the relative abundance of the feature.
  • In prevalence models, a one-unit change in the metadatum variable corresponds to a
    coef change in the log-odds of a feature being present.
• Model: specifies whether the association is abundance or prevalence.
• N: the total number of samples used in the model for this association (since minimum abundance/prevalence can exclude samples from comparisons).
• N not Zero: the total of number of these samples in which the feature is non-zero.
• P-value: the nominal significance of this association.
• Q-value: the corrected significance is computed with p.adjust with the correction method (BH, etc.).

Heatmap

This figure contain a combined coefficient plot and heatmap of the top 25 (unless otherwise specified) significant associations. In the heatmap, one star indicates the individual q-value is below the parameter max_significance, and two stars indicate the individual q-value is below max_significance divided by 10.

Box and Scatter Plots

A tab is presented for each Fixed Effect, which includes plots for each of the significant associations in the Association Results (boxplots for categorical variables, scatter plots for continuous).

Scatter plots are used for continuous metadata abundance associations.

Box plots are used for categorical data abundance associations.

Box plots are used for continuous data prevalence associations.

Grids are used for categorical data prevalence associations.

Data points plotted are after filtering, normalization, and transformation so that the scale in the plot is the scale that was used in fitting.

At the top right of each association plot is the name of the significant association in the results file, the FDR corrected q-value for the individual association, the number of samples in the dataset, and the number of samples with non-zero abundances for the feature. In the plots with categorical metadata variables, the reference category is on the left, and the significant q-values and coefficients in the top right are in the order of the values specified above. Because the displayed coefficients correspond to the full fit model with (possibly) scaled metadata variables, the marginal association plotted might not match the coefficient displayed. However, the plots are intended to provide an interpretable visual while usually agreeing with the full model.

Volcano

Volcano plot depicting all significant variables for each fixed effect

Forest

Forest plot helps to visually summarize the significant features effect size from the model contrasts along with their confidence intervals.

X-axis represents the contrast effect size; Y-axis represents the significant features that were found in respective contrasts of interest. The dot and the lines from the dot represents the individual feature’s effect size and the confidence interval of the effect size respectively

Exporting the Data

All data can be exported as a .ZIP file by navigating to the comparative analysis and selecting the "Export" button in the top right corner. This .ZIP file will contain all input tables, results table, all figures (PDF), and a maaslin3.log for debugging purposes.