plot_heatmap: Plot heatmap

plot_heatmapR Documentation

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/importomics documentation built on July 11, 2024, 11:26 a.m.