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

In CharlieCarpenter/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)

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