relabu_heatmap {animalcules}R Documentation

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"), 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')

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


[Package animalcules version 1.0.4 Index]