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