amp_correlation: Generates correlation networks from amplicon data.
In MadsAlbertsen/ampvis: Tools for visualising amplicon data

A nice long description

1	amp_correlation(data)

`data`	(required) A phyloseq object including sample data.
`trans`	Transform the raw counts by "sqrt".
`treshold.cor`	Absolute correlation treshold (default: 0.8).
`treshold.pval`	P-value treshold for correlations (default: 0.01).
`ignore.zero`	Remove observations where 1 obeservation has 0 counts from the correlation test (default: F)
`ignore.global.zero`	Remove observations where 1 obeservation has 0 counts from the initial correlation test (default: T)
`scale.seq`	The number of sequences in the pre-filtered samples (default: 20000)
`treshold.abundance`	Average abundance treshold (default: 0)
`treshold.obs`	Minimum number of observations in order to calculate correlations (default: 10).
`label`	Plot taxonomic classifications (e.g. "Genus") instead of points.
`scale.abundance`	Scale the size of nodes by abundance (default: F).
`output`	Either plot or complete (default: "plot").
`treshold.count`	Minimum count in order to use a pair of observations for test of correlation (default: 10)
`scale.size`	Scale the size of the plotted objects (default: 1)
`tax.class`	Converts a specific phyla to class level instead (e.g. "p__Proteobacteria").
`tax.empty`	Either "remove" OTUs without taxonomic information, add "best" classification or add the "OTU" name (default: best).
`tax.aggregate`	The taxonomic level that the data should be aggregated to (default: OTU).
`alpha`	Transparency of the plotted points (default: 1).