Try this app if you get errors with tax_fix() that are tricky to work past,
or suggestions to use tax_fix() that you don't understand.
The app shows you the tax_table of your data (searchable) with unknown values highlighted.
It allows you to interactively modify minimum allowed length and to select further values to be defined as unknown.
It will show you the correct tax_fix() code to copy paste into your script
to reproduce the interactive filtering.
tax_fix_interactive(data, app_options = list(launch.browser = TRUE))nothing
tax_fix for the non-interactive function to use in your scripts
library(dplyr)
library(phyloseq)
# create some problem-filled example tax_table data
data(dietswap, package = "microbiome")
ps <- dietswap
# create unknowns to test filling
tt <- tax_table(ps)
ntax <- ntaxa(ps)
set.seed(123)
g <- sample(1:ntax, 30)
f <- sample(g, 10)
p <- sample(f, 3)
tt[g, 3] <- "g__"
tt[f, 2] <- "f__"
tt[p, 1] <- "p__"
tt[sample(1:ntax, 10), 3] <- "unknown"
# create a row with only NAs
tt[1, ] <- NA
tax_table(ps) <- tax_table(tt)
# function takes a phyloseq and shows code for how to fix the tax_table
# tax_fix_interactive(data = ps)