plot_volcano: Plot volcano

In bhagwataditya/autonomics: Unified Statistical Modeling of Omics Data

Plot volcano

Description

Plot volcano

Usage

plot_volcano(
  object,
  fit = fits(object)[1],
  coefs = setdiff(autonomics::coefs(object, fit = fit), "Intercept")[1],
  facet = if (is_scalar(fit)) "coef" else c("fit", "coef"),
  scales = "fixed",
  shape = if ("imputed" %in% fvars(object)) "imputed" else NULL,
  size = NULL,
  alpha = NULL,
  label = "feature_id",
  max.overlaps = 10,
  features = NULL,
  nrow = length(fit),
  p = 0.05,
  fdr = 0.05,
  xndown = NULL,
  xnup = NULL,
  title = NULL
)

Arguments

object	SummarizedExperiment
fit	'limma', 'lme', 'lm', 'wilcoxon'
coefs	character vector
facet	character vector
scales	'free', 'fixed', etc.
shape	fvar (string)
size	fvar (string)
alpha	fvar (string)
label	fvar (string)
max.overlaps	number: passed to ggrepel
features	feature ids (character vector): features to encircle
nrow	number: no of rows in plot
p	number: p cutoff for labeling
fdr	number: fdr cutoff for labeling
xndown	x position of ndown labels
xnup	x position of nup labels
title	string or NULL

Value

ggplot object

Examples

# Regular Usage
    file <- system.file('extdata/atkin.metabolon.xlsx', package = 'autonomics')
    object <- read_metabolon(file)
    object %<>% fit_limma()
    object %<>% fit_lm()
    plot_volcano(object, coefs = 't3-t0', fit = 'limma')                   # single contrast
    plot_volcano(object, coefs = c('t2-t0', 't3-t0'), fit = 'limma')          # multip contrasts
    plot_volcano(object, coefs = c('t2-t0', 't3-t0'), fit = c('limma', 'lm')) # multip contrs & methods

# When nothing passes FDR
    fdt(object) %<>% add_adjusted_pvalues('fdr', fit = 'limma',coefs = 't3-t0')
    object %<>% extract( fdrvec(object, fit = 'limma', coef = 't3-t0') > 0.05, )
    plot_volcano(object, coefs = 't3-t0', fit = 'limma')

# Additional mappings
    file <- system.file('extdata/fukuda20.proteingroups.txt', package = 'autonomics')
    object <- read_maxquant_proteingroups(file, impute = TRUE)
    object %<>% fit_limma()
    plot_volcano(object)
    plot_volcano(object, label = 'gene')
    plot_volcano(object, label = 'gene', size = 'log2maxlfq')
    plot_volcano(object, label = 'gene', size = 'log2maxlfq', alpha = 'pepcounts')
    plot_volcano(object, label = 'gene', features = c('Q503D2_DANRE'))
    plot_volcano(object, label = 'gene', features = list(c('Q503D2_DANRE', 'Q6DGK4_DANRE'), 
                                                         c('Q6DGK4_DANRE', 'F1Q7L0_DANRE')))

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