relabu_boxplot: Plot boxplots comparing different organism prevalence across...
In hiplot/animalcules: Interactive microbiome analysis toolkit

Description Usage Arguments Value Examples

Plot boxplots comparing different organism prevalence across conditions

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

`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

A plotly object

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