physeq.mra.prevalence | R Documentation |
A comprehensive relative abundance function for phyloseq objects. Includes output of relative abundance summary statistics (mean relative abundance and prevalence), both as a dataframe and with an added option for plotting. The function accepts input of count or relative abundance data.
physeq.mra.prevalence(physeq, type, vis.export = TRUE, export_prefix.in)
physeq |
Input phyloseq object |
type |
One of |
vis.export |
|
export_prefix.in |
Provide a prefix (string) for summary plots if vis.export = |
If count data is input, it will be first converted to relative abundance. The relative abundance phyloseq object and OTU table will also be returned.
List containing [1] mean relative abundance and prevalence for each taxa (dataframe) [2] Relative abundance OTU table (dataframe) [3] Relative abundance phyloseq object. If vis.export = TRUE Will also export summary plots of mean relative abundance and prevalence distributions to working directory
physeq.mra.prevalence(physeq = dat, type = "counts", vis.export = TRUE, export_prefix.in = "test_counts") #with export physeq.mra.prevalence(physeq = dat_rel, type = "relabund") #input phyloseq object with relative abundance
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.