Plot boxplots comparing different organism prevalence across conditions

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')
#> Using Row.names, SEX as id variables
p
#> Warning: minimal value for n is 3, returning requested palette with 3 different levels
#> Warning: minimal value for n is 3, returning requested palette with 3 different levels
#> Warning: 'layout' objects don't have these attributes: 'boxmode'
#> Valid attributes include:
#> 'font', 'title', 'uniformtext', 'autosize', 'width', 'height', 'margin', 'computed', 'paper_bgcolor', 'plot_bgcolor', 'separators', 'hidesources', 'showlegend', 'colorway', 'datarevision', 'uirevision', 'editrevision', 'selectionrevision', 'template', 'modebar', 'newshape', 'activeshape', 'meta', 'transition', '_deprecated', 'clickmode', 'dragmode', 'hovermode', 'hoverdistance', 'spikedistance', 'hoverlabel', 'selectdirection', 'grid', 'calendar', 'xaxis', 'yaxis', 'ternary', 'scene', 'geo', 'mapbox', 'polar', 'radialaxis', 'angularaxis', 'direction', 'orientation', 'editType', 'legend', 'annotations', 'shapes', 'images', 'updatemenus', 'sliders', 'colorscale', 'coloraxis', 'metasrc', 'barmode', 'bargap', 'mapType'