Alpha Diversity
Investigate the OTU/Taxonomic richness of the OTU table. This analysis uses the diversity measure from the R 'vegan' package here
Used For
Comparisons of alpha diversity measures with one or more sample groups (boxplot)
Comparisons of alpha diversity measures with a quantitative metadata variable (scatterplot)
Visualization Parameters
Taxonomic Level
The taxonomic level to aggregate the OTUs at. The OTUs will be grouped together (by summing the OTU values) at the selected taxonomic level before the analysis is applied.
Experimental Variable
The metadata variable to compare the alpha diversity against.
Plot Type
Whether to compare the alpha diversity using a boxplot or scatterplot. Mian tries to automatically determine the correct visualization type basd on the data.
Diversity Context
Alpha Diversity The diversity measure based on the diversity index above
Evenness Pielou's evenness measure as calculated here
OTU/Taxonomic Richness The number of unique species within each sample
Diversity Index
Indicate the method by which the alpha diversity should be calculated. More information on the different diversity types can be found here Faith's Phylogenetic Diversity is a taxonomic richness analogue based on the phylogenetic tree
Statistical Test
The selected test is automatically applied between every sample group.
Wilcoxon Rank-Sum A non-parametric test to test whether a randomly selected sample from one group will be different from a randomly selected sample from another group
Welch's T-Test A parametric test to test whether two populations have equal means
ANOVA A parametric test to test whether two populations have equal means
Interactive Elements
Hover over each point to determine its sample ID and its value
Zoom or pan on the scatterplot view
Additional Features
Save Snapshot: Save the visualization to the experiment notebook
Download: Downloads the visualization as a PNG file
Share: Creates a shareable link that allows you to share the visualization with others
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