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head(asv_table)

The taxonomy data from ampliseq is prefaced by D_0_D_1_ etc but ampvis2 expects taxonomy assignments to be k_p_, etc (kingdom, phylum, etc). So we need to convert these using gsub()

asv_table$Kingdom <- gsub("D_0", "k", asv_table$Kingdom)
asv_table$Phylum <- gsub("D_1", "p", asv_table$Phylum)
asv_table$Class <- gsub("D_2", "c", asv_table$Class)
asv_table$Order <- gsub("D_3", "o", asv_table$Order)
asv_table$Family <- gsub("D_4", "f", asv_table$Family)
asv_table$Genus <- gsub("D_5", "g", asv_table$Genus)
asv_table$Species <- gsub("D_6", "s", asv_table$Species)

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Now you need to choose a secondary variable, to split you plots by (change "Phase" to your secondary variable name).

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You can see all the available variables you can choose from by looking at your samples_table column names

colnames(samples_table)

Select the secondary variable.

var2 <- "Batch"

IMPORTANT: your plots will be split into as many facets as there are unique subcategories in your secondary variable. To see how many subcategories:

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