ampvis2 rank abundance plot (version 2.8.9+galaxy0)

Ampvis2 RDS dataset:

Generated with ampvis2: load

Metadata list:

Group the samples by:

In order to select values a metadata list needs to be selected first.

Show standard deviation:

Log10-transform the x-axis:

Often most variation is observed among the most abundant OTU's, log10-transforming the x-axis will highlight this better.

Output options

Output options 0

What it does

Generates a rank abundance curve (rank abundance vs cumulative read abundance), optionally with standard deviation from mean intervals.

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

Currently only OTU level is supported.

Input

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

The metadata list output of the ampvis2: load tool (or ampvis2: mergereplicates or the ampvis2: subset sample tool). This input is only used for providing values to the parameters alowing to select metadata variables or values.

Output

An rank abundance plot in the chosen output format.