ampvis2 alpha diversity (version 2.8.9+galaxy1)

Ampvis2 RDS dataset:

Generated with ampvis2: load

Alpha-diversity measure(s) to be included:

Calculate sample richness estimates:

Chao1 and ACE

Rarefy species richness to this value:

before calculating alpha diversity and/or richnes

Group by metadata field (for plotting):

Specify the metadata field to group the plot by

Scatter plot instead of boxplot?:

Select to generate a scatter plot instead of a boxplot

Output options

Output options 0

What it does

Calculate alpha-diversity indices for each sample and combines with the metadata.

The Galaxy tool calls the amp_alpha_diversity function of the ampvis2 package.

Usage

The alpha-diversity indices are calculated per sample using the vegan function diversity, where the read abundances are first rarefied using rrarefy by the size of the rarefy argument. Refer to the vegan documentation for details about the different indices and how they are calculated.

Input

An ampvis2 RDS dataset obtained by the ampvis2: load tool (or ampvis2: mergereplicates or one of the ampvis2: subset ... tools).

Output

A tabular dataset containing the chosen alpha-diversity measures per sample.