plot_exprs_per_coef: Plot exprs per coef

In bhagwataditya/autonomics: Unified Statistical Modeling of Omics Data

Plot exprs per coef

Description

Plot exprs per coef

Usage

plot_exprs_per_coef(
  object,
  fit = fits(object)[1],
  coefs = default_coefs(object, fit = fit),
  x = default_x(object),
  block = NULL,
  geom = default_geom(object, x, block = block),
  orderbyp = FALSE,
  title = x,
  subtitle = default_subtitle(fit, x, coefs),
  n = 1,
  nrow = 1,
  ncol = NULL,
  theme = ggplot2::theme(legend.position = "bottom", legend.title = element_blank(),
    plot.title = element_text(hjust = 0.5), plot.subtitle = element_text(hjust = 0.5))
)

Arguments

object	SummarizedExperiment
fit	'limma', 'lm', 'lme', 'lmer', 'wilcoxon'
coefs	subset of coefs(object) to consider in selecting top
x	x svar
block	group svar
geom	'boxplot' or 'point'
orderbyp	TRUE or FALSE
title	string
subtitle	string
n	number
nrow	number of rows in faceted plot
ncol	number of cols in faceted plot
theme	ggplot2::theme(...) or NULL

Value

ggplot object

See Also

plot_sample_densities, plot_sample_violins

Examples

file <- system.file('extdata/atkin.metabolon.xlsx', package = 'autonomics')
object <- read_metabolon(file)
object %<>% fit_limma()
object %<>% pls(by = 'subgroup')
object %<>% pls(by = 'Diabetes')
object %<>% pls(by = 'Subject')
plot_exprs_per_coef(object)
plot_exprs_per_coef(object, orderbyp = TRUE)
plot_exprs_per_coef(object, fit = 'pls1', block = 'Subject')

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