adonis_to_table: Quick wrapper to format PERMANOVA results

In g-antonello/gautils: An R package for quick microbiome data wrangle and visualization

Quick wrapper to format PERMANOVA results

Description

Quick wrapper to format PERMANOVA results

Usage

adonis_to_table(adonis.out, adjR2 = TRUE, new_rownames = NA)

Arguments

adonis.out	A adonis2 output object as is
adjR2	A logical, should another column be calculated with the adjusted R squared? the thing is calculated with vegan::RsquareAdj
new_rownames	A character vector containing prettier variable names, which will be passed with set_rownames

Value

A data.frame Ready to be passed to kable/DT/flextable

Examples

library(gautils)
data(enterotype)
distMat <-  phyloseq::distance(microbiome::transform(enterotype, "compositional"), "bray")

adonisObj <- adonis2(distMat ~ SeqTech + Enterotype, by = "margin", permutations = 2000, data = microbiome::meta(enterotype), na.action = na.omit)

adonis_as_table <- adonis_to_table(adonisObj)
adonis.kbl <- kableExtra::kbl(adonis_as_table, digits = 2) %>%
kableExtra::kable_styling()

adonis_as_table2 <- adonis_to_table(adonisObj, new_rownames = c("Sequencing Techonology", "Enterotype Code"))
adonis.kbl2 <- kableExtra::kbl(adonis_as_table2, digits = 2) %>%
kableExtra::kable_styling()

g-antonello/gautils documentation built on May 3, 2024, 10:51 a.m.