ra_bars: Function to make stacked bar charts of taxa relative...

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

Description

A function to make stacked bar charts of taxa relative abuncance with the choice to stratify by a variable of interest

Usage

ra_bars(
  micro_set,
  table,
  ...,
  top_taxa = 0,
  RA = 0,
  specific_taxa,
  main,
  subtitle,
  ylab,
  xlab,
  xaxis,
  lines = TRUE
)

Arguments

micro_set	A tidy_micro data set
table	OTU table you'd like to use when calculating alpha diversity. Your lowest level is recommended
...	A categorical variable by which you'd like to stratify your relative abundances
top_taxa	Only plot X taxa with the highest relative abundance. The rest will be aggregated into an "Other" category.
RA	Only plot taxa with a relative abundance higher than X. The rest will be aggregated into an "Other" category.
specific_taxa	Plot this specific taxa even if it doesn't meet the top_taxa or RA requirements
main	Plot title
subtitle	Subtitle for the plot
ylab	y-axis label
xlab	x-axis label
xaxis	Labels for the x-axis ticks. Most useful for categorical variables and defaults to the levels
lines	Logical; Add outlines around the different taxa colors in the stacked bar charts

Value

Returns 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

## Full cohort abundance
set %>%
ra_bars(table = "Family", top_taxa = 10)

## Stratified by variable of interest
set %>%
ra_bars(table = "Family", bpd1, top_taxa = 10)

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