sample_color_order argument in amp_ordinate

[slambrechts]

Hi there, I was wondering how to use the argument sample_color_order in amp_ordinate? Could you please give an example?

[KasperSkytte]

Hi

It simply sets the factor levels of the particular metadata variable set by the sample_color_by argument. An example below.

library(ampvis2)
#> Loading required package: ggplot2
#subset to one WWTP
d <- amp_subset_samples(AalborgWWTPs, Plant %in% "Aalborg West")
#> 35 samples and 2596 OTUs have been filtered 
#> Before: 67 samples and 9430 OTUs
#> After: 32 samples and 6834 OTUs

#plot with default color order of the sample_color_by argument
amp_ordinate(d, 
             type = "pcoa",
             transform = "none",
             filter_species = 0,
             num_threads = 30,
             distmeasure = "wunifrac",
             sample_color_by = "Period")

#plot with custom color order of the sample_color_by argument
##levels of metadata variable (even if not factor)
unique(AalborgWWTPs$metadata$Period)
#> [1] "Winter" "Spring" "Summer" "Fall"
#reorder and plot with new color order
newlevels <- unique(AalborgWWTPs$metadata$Period)[c(2,3,4,1)]
amp_ordinate(d, 
             type = "pcoa",
             transform = "none",
             filter_species = 0,
             num_threads = 30,
             distmeasure = "wunifrac",
             sample_color_by = "Period",
             sample_color_order = newlevels)

^{Created on 2020-03-02 by the reprex package (v0.3.0)}

So you could also just set factor levels on the particular metadata variable manually if that's more transparent for you.