...

tiff_exp <- paste0("community_tax_abund_BW_plot_", taxgroup, "_samples_.tiff")
ggsave(file = tiff_exp, dpi = 300, compression = "lzw", device = "tiff", plot = p, width = 20, height = 20, units = "cm")
pdf_exp <- paste0("community_tax_abund_BW_plot_", taxgroup, "_samples_.pdf")
ggsave(file = pdf_exp, device = "pdf", plot = p, width = 20, height = 20, units = "cm")

5a. Choosing a variable to analyse

In the Alpha Diversity section, you already imported your nfcore/ampliseq results and converted them to an ampvis2 object. To have another quick look at your ampvis object:

ampvisdata

As in the Alpha Diversity section, you need to choose a variable to work with.

You can view your variables as column names in your samples_table:

colnames(samples_table)

Now enter the variable you want to analyse:

group <- "Nose_size"