relabu_barplot {animalcules}R Documentation

Plot bar plots of sample and group level relative abundance

Description

Plot bar plots of sample and group level relative abundance

Usage

relabu_barplot(MAE, tax_level, order_organisms = c(),
  sort_by = c("nosort", "conditions", "organisms"),
  group_samples = FALSE, group_conditions = "ALL",
  sample_conditions = c(), isolate_samples = c(),
  discard_samples = c(), show_legend = TRUE)

Arguments

MAE

A multi-assay experiment object

tax_level

The taxon level used for organisms

order_organisms

A character list of organisms to send to top

sort_by

Sort bars by one of c("nosort", "conditions", "organisms")

group_samples

A bool specifying whether to group samples

group_conditions

Group by one or more conditions e.g. "ALL" or "SEX"

sample_conditions

Plot associatied conditions with samples.

isolate_samples

Isolate specific samples e.g. c("SAM_01", "SAM_02")

discard_samples

Discard specific samples e.g. c("SAM_01", "SAM_02")

show_legend

A bool specifying whether or not to show organisms legend

Value

A plotly object

Examples

data_dir = system.file("extdata/MAE.rds", package = "animalcules")
toy_data <- readRDS(data_dir)
p <- relabu_barplot(toy_data,
                    tax_level="family",
                    order_organisms=c('Retroviridae'),
                    sort_by="organisms",
                    sample_conditions=c('SEX', 'AGE'),
                    show_legend=TRUE)
p


[Package animalcules version 1.0.5 Index]