relabu_heatmap: Plot heatmap of sample level counts in logcpm

In compbiomed/animalcules: Interactive microbiome analysis toolkit

Plot heatmap of sample level counts in logcpm

Description

Plot heatmap of sample level counts in logcpm

Usage

relabu_heatmap(
  MAE,
  tax_level,
  sort_by = c("nosort", "conditions", "organisms", "alphabetically"),
  sample_conditions = c(),
  isolate_organisms = c(),
  isolate_samples = c(),
  discard_samples = c(),
  log_cpm = TRUE
)

Arguments

MAE	A multi-assay experiment object
tax_level	The taxon level used for organisms
sort_by	Sort bars by one of c('nosort', 'conditions', 'organisms', 'alphabetically')
sample_conditions	Plot conditions e.g. c('SEX', 'AGE')
isolate_organisms	Isolate specific organisms e.g. c('Hepacivirus')
isolate_samples	Isolate specific samples e.g. c('SAM_01', 'SAM_02')
discard_samples	Discard specific samples e.g. c('SAM_01', 'SAM_02')
log_cpm	Convert counts to logcpm

Value

A plotly object

Examples

data_dir <- system.file("extdata/MAE.rds", package = "animalcules")
toy_data <- readRDS(data_dir)
p <- relabu_heatmap(toy_data,
  tax_level = "genus",
  sort_by = "conditions",
  sample_conditions = c("SEX", "AGE")
)
p

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