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

In CharlieCarpenter/tidy.micro: 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

Value

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

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) %>%
filter(day == 7) ## Only including the first week

set %>% taxa_boxplot("Firmi:Clost:Clostridiales", bpd1)

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