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

In compbiomed/animalcules: Interactive microbiome analysis toolkit

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", "alphabetically"),
  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", "alphabetically")
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

compbiomed/animalcules documentation built on Feb. 7, 2024, 12:13 p.m.