If you have problems or questions, ideas for improvements, or even found a bug or two, feel free to post at https://github.com/MadsAlbertsen/ampvis2/issues or email one of the developers, anything and everything is welcome.
By default the raw read counts in the abundance matrix are normalised (transformed to percentages) by some plotting functions automatically (for example
amp_timeseries, and more). This means that the relative abundances shown will be calculated based on the remaining taxa after the subset, not including the removed taxa, if any. To circumvent this, set
normalise = TRUE when subsetting with the
amp_subset_samples functions, and then set
raw = TRUE in the plotting function. This will transform the OTU counts to relative abundances BEFORE the subset, and setting
raw = TRUE will skip the transformation in the plotting function, see the example below.
If you wan’t to calculate a distance matrix manually and use it for PCoA in
amp_ordinate, it can be done quite easily by just setting
filter_species = 0,
transform = "none", and
distmeasure = "none", like below. The matrix should be a symmetrical matrix containing coefficients for all pairs of samples in the data. This is not ideal for nMDS since it is not an eigenvalue based method, but if you really want, set
distmeasure = "euclidean" instead.
#Override the abundance table in the ampvis2 object with a custom distance matrix ampvis2_object$abund <- custom_dist_matrix #set filter_species = 0, transform = "none", and distmeasure = "none" amp_ordinate(ampvis2_object, type = "pcoa", filter_species = 0, transform = "none", distmeasure = "none")
Simply source the
phyloseq_to_ampvis2() function from this gist, either by copy/pasting into R, or by using
devtools::source_gist() as shown below. You need both the
ampvis2 packages installed for it to work.