PERMANOVA final output table

[artur-sannikov]

We had a short discussion on Mattermost about it.

Currently in the chapter on the community
similarity,
we use getPERMANOVA function to output it into a separate object. We can also
use addPERMANOVA() function to add it directly to metadata of TreeSE (see
docs):

tse <- addPERMANOVA(
    tse,
    assay.type = "relabundance",
    method = "bray",
    formula = x ~ SampleType,
    permutations = 99
    )
# The results are stored to metadata
metadata(tse)[["permanova"]]

We can rewrite that part by using addPERMANOVA().

For my own project I wrote this function, which can be used to output the
final table in Quarto document.

library(mia)
library(janitor)
library(tidyverse)
library(knitr)
library(kableExtra)

outputFullPermanova <- function(x) {
  x$permanova |>
    as.data.frame() |>
    slice(1:3) |>
    rename(p_val = "Pr(>F)") |>
    cbind(
      x$homogeneity |>
        rename("p_homogeneity" = "Pr(>F)")
    ) |>
    clean_names() |>
    rownames_to_column("variable") |>
    select(variable, r2, p_val, p_homogeneity) |>
    mutate(
      variable = str_to_title(variable)
    ) |>
    kable(
      digits = 3,
      row.names = FALSE,
      booktabs = TRUE,
      col.names = c("Variable", "R2", "P", "P Homogeneity")
    ) |>
    kable_styling(latex_options = c("hold_position", "striped"), font_size = 8)
}