make_ord_df: Make a data frame of the ordination
In JCSzamosi/aftersl1p: Generate Summary Graphics and Basic Analysis of 16s Data

make_ord_df

R Documentation

Make a data frame of the ordination

Description

Take a phyloseq object and generate a data frame of the distance-based ordination of the samples for plotting. This function has been tested with ordination methods 'PCoA' and 'RDA'. I can't make any promises if you use a different ordination method.

Usage

make_ord_df(
  physeq,
  dist_meth = "bray",
  ord_meth = "PCoA",
  scree_only = FALSE,
  axes = 1:4
)

Arguments

`physeq`	A phyloseq object with an OTU table and sample data. The table should be normalized (rarefied, relative abundance, some kind of log-ratio transformation) so that the distance metrics will be meaningful. Make sure that the transformation you have used is appropriate for the distance method you choose.
`dist_meth`	The distance method to be use. Must be one of the methods accepted by the `phyloseq::distance()` function. Default is 'bray'. If 'jaccard' is used, adds the `binary = TRUE` argument. If you have taken a clr transform of your data and want Aitchison distances, choose `'euclidean'`. Currently, tree-based methods like `'unifrac'` and `'wunifrac'` are not supported.
`ord_meth`	The ordination method. Must be one of the methods accepted by the `phyloseq::ordinate()` function. Default is 'PCoA'. Make sure the ordination method you choose is appropriate for your distance method.
`scree_only`	If `TRUE`, this function will print the scree plot of the requested ordination and then exit. Good for deciding how many axes you care about. Default is `FALSE`.
`axes`	A vector of integers indicating which ordination axes to include in the data frame. Defaults to `1:4`.