plot_summary: Plot summary

In bhagwataditya/autonomics: Unified Statistical Modeling of Omics Data

Plot summary

Description

Plot summary

Usage

plot_summary(
  object,
  fit = "limma",
  formula = default_formula(object),
  block = NULL,
  label = "feature_id",
  palette = make_svar_palette(object, svar = svar)
)

Arguments

object	SummarizedExperiment
fit	linmod engine : 'limma', 'lm', 'lme', 'lmer' or 'wilcoxon'
formula	model formula
block	NULL or svar
label	fvar
palette	NULL or colorvector

Examples

file <- system.file('extdata/atkin.metabolon.xlsx', package = 'autonomics')
object <- read_metabolon(file)
object %<>% pca()
object %<>% pls(by = 'subgroup')
object %<>% fit_limma()
plot_summary(object, block = 'Subject')

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