plot_heatmap: Plot heatmap

In bhagwataditya/autonomics: Unified Statistical Modeling of Omics Data

Plot heatmap

Description

Plot heatmap

Usage

plot_heatmap(
  object,
  fit = fits(object)[1],
  coef = default_coefs(object, fit = fit)[1],
  effectsize = 0,
  p = 1,
  fdr = 0.05,
  n = 100,
  assay = assayNames(object)[1],
  cluster_features = FALSE,
  cluster_samples = FALSE,
  flabel = intersect(c("gene", "feature_id"), fvars(object))[1],
  group = "subgroup",
  verbose = TRUE
)

Arguments

object	SummarizedExperiment
fit	'limma', 'lm', 'lme(r)', 'wilcoxon'
coef	string: one of coefs(object)
effectsize	number: effectsize filter
p	number: p filter
fdr	number: fdr filter
n	number: n filter
assay	string: one of assayNames(object)
cluster_features	TRUE or FALSE
cluster_samples	TRUE or FALSE
flabel	string: feature label
group	sample groupvar
verbose	TRUE or FALSE

Examples

file <- system.file('extdata/fukuda20.proteingroups.txt', package = 'autonomics')
object <- read_maxquant_proteingroups(file, fit = 'limma')
plot_heatmap(object)

bhagwataditya/autonomics documentation built on Dec. 1, 2024, 12:27 a.m.