pull_lev: Shorten long taxa names

In CharlieCarpenter/tidyMicro: A Pipeline for Microbiome Analysis and Visualization

Description

pull_lev is designed to work with Taxa names that contain multiple taxonomy levels. The function splits Taxa names using str_split, then grabs the string in position l or higher. If nothing exists at or past position l, the function will add "Unclassified" to the last position. The function skips over any Taxa named "Other".

Usage

pull_lev(Taxa, l, sep = "/")

Arguments

Taxa	Taxa names with taxonomic rank separated by some character
l	Numeric. Position / taxonomic rank. Best if it is the highest rank in Taxa names
sep	Character to split

Value

A character string

Examples

data(bpd_fam); data(bpd_clin)
set <- tidy_micro(otu_tabs = bpd_fam, clinical = bpd_clin, tab_names = "Family",
prev_cutoff = 5, ra_cutoff = 1, exclude_taxa = "Bacteria",
count_summary = FALSE, filter_summary = FALSE) %>%
filter(day == 7)

## Taxa names
pull_lev(unique(set$Taxa), 4)

## Most useful to clean up plots ##

# Hard to read!
(ch <- cor_heatmap(set, table = "Family", weight, gestational_age))

# Much better
ch$data$Taxa <- pull_lev(ch$data$Taxa,4)
ch

CharlieCarpenter/tidyMicro documentation built on April 25, 2021, 4:09 p.m.