relabu_boxplot: Plot boxplots comparing different organism prevalence across...

In animalcules: Interactive microbiome analysis toolkit

Description

Plot boxplots comparing different organism prevalence across conditions

Usage

relabu_boxplot(
  MAE,
  tax_level,
  condition,
  organisms = c(),
  datatype = c("counts", "relative abundance", "logcpm")
)

Arguments

MAE	A multi-assay experiment object
tax_level	The taxon level used for organisms
condition	Compare groups by condition e.g. 'SEX'
organisms	Include organisms for plotting.
datatype	counts, relative abundance,logcpm

Value

A plotly object

Examples

data_dir = system.file('extdata/MAE.rds', package = 'animalcules')
toy_data <- readRDS(data_dir)
p <- relabu_boxplot(toy_data,
                    tax_level='genus',
                    organisms=c('Escherichia', 'Actinomyces'),
                    condition='SEX',
                    datatype='logcpm')
p

animalcules documentation built on Nov. 8, 2020, 6:47 p.m.