relabu_barplot: Plot bar plots of sample and group level relative abundance

In animalcules: Interactive microbiome analysis toolkit

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

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