taxa_summary: Summarize the information

In CharlieCarpenter/tidy.micro: A Pipeline For Microbiome Analysis And Visualization

Description

Give taxa summary table stratified by variables of interest and/or OTU tables

Usage

taxa_summary(micro_set, ..., table = NULL, obj = ra, taxa = TRUE)

Arguments

micro_set	A tidy_micro data set
...	Covariates of interest
table	OTU table of interest. If NULL, all tables will be used
obj	The taxonomic information of interest
taxa	Logical; Whether or not to stratify by taxa

Value

A tibble containing columns of stratifying variables and several summary columns

Examples

data(phy); data(cla); data(ord); data(fam); data(met)

otu_tabs <- list(Phylum = phy, Class = cla, Order = ord, Family = fam)
set <- tidy_micro(otu_tabs = otu_tabs, meta = met) %>%
mutate(bpd1 = factor(bpd1))

## Summarize each taxa by Table
set %>% taxa_summary

## Summarize each taxa by a categorical variable of interest
set %>% taxa_summary(bpd1)

## Summarize each taxa by a categorical variable of interest within a Table
set %>% taxa_summary(bpd1, table = "Phylum")

## Summarize within group or table only
set %>% taxa_summary(taxa = FALSE)

CharlieCarpenter/tidy.micro documentation built on Jan. 19, 2020, 6:28 p.m.