taxa_boxplot: Function to make boxplots of taxa counts or relative...

In tidyMicro: A Pipeline for Microbiome Analysis and Visualization

Description

A function to make boxplots of one specified taxa relative abundance with the option to stratify by a factor variable

Usage

taxa_boxplot(
  micro_set,
  taxa,
  ...,
  y = ra,
  xlab = NULL,
  ylab = NULL,
  main = NULL,
  subtitle = NULL,
  legend_title = NULL
)

Arguments

micro_set	A tidy_micro data set
taxa	A character string. The name of the taxa of interest
...	The factor variable you'd like to stratify by
y	The taxa information
xlab	x-axis label
ylab	y-axis label
main	Plot title
subtitle	Subtitle for the plot
legend_title	Title of plot legend

Value

A ggplot that you can add geoms to if you'd like

Examples

data(bpd_phy); data(bpd_cla); data(bpd_ord); data(bpd_fam); data(bpd_clin)

otu_tabs <- list(Phylum = bpd_phy, Class = bpd_cla,
Order = bpd_ord, Family = bpd_fam)
set <- tidy_micro(otu_tabs = otu_tabs, clinical = bpd_clin) %>%
filter(day == 7) ## Only including the first week

set %>%
taxa_boxplot("Firmicutes/Bacilli/Bacillales/Staphylococcaceae", bpd1)

Example output

Loading required package: tidyverse
── Attaching packages ─────────────────────────────────────── tidyverse 1.3.0 ──
✔ ggplot2 3.3.2     ✔ purrr   0.3.4
✔ tibble  3.0.4     ✔ dplyr   1.0.2
✔ tidyr   1.1.2     ✔ stringr 1.4.0
✔ readr   1.4.0     ✔ forcats 0.5.0
── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag()    masks stats::lag()
Contains 74 libraries from OTU files.

Summary of sequencing depth:
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
   8851   24938   33314   36650   43590   97408 

tidyMicro documentation built on Jan. 13, 2021, 6:18 a.m.