plot_volcano: Plot volcano

plot_volcanoR Documentation

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('hmbsb'))

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