PomaVolcano: Volcano Plot

In POMA: User-friendly Workflow for Pre-processing and Statistical Analysis of Mass Spectrometry Data

Description

PomaVolcano() generates a volcano plot from the PomaUnivariate(method = "ttest") result. The data can't have negative values.

Usage

PomaVolcano(
  data,
  pval = "raw",
  pval_cutoff = 0.05,
  adjust = "fdr",
  log2FC = 0.6,
  xlim = 2,
  labels = FALSE,
  paired = FALSE,
  var_equal = FALSE,
  interactive = FALSE,
  plot_title = TRUE
)

Arguments

data	A MSnSet object. First pData column must be the subject group/type. Only for two group data!
pval	Select a pvalue type to generate the volcano plot. Options are: "raw" and "adjusted".
pval_cutoff	Numeric. Define the pvalue cutoff (horizontal line).
adjust	Multiple comparisons correction method for t test result. Options are: "fdr", "holm", "hochberg", "hommel", "bonferroni", "BH" and "BY".
log2FC	Numeric. Define the log2 fold change cutoff (vertical lines).
xlim	Numeric. Define the limits for x axis.
labels	Logical that indicates if selected labels will be plotted or not. Defaul is FALSE.
paired	Logical that indicates if the data is paired or not.
var_equal	Logical that indicates if the data variance is equal or not.
interactive	Logical that indicates if an interactive plot will be plotted or not. Defaul is FALSE.
plot_title	Logical that indicates if title will be plotted or not. Defaul is TRUE.

Value

A ggplot2 object.

Author(s)

Pol Castellano-Escuder

Examples

data("st000336")

st000336 %>% 
  PomaImpute() %>%
  PomaVolcano()

POMA documentation built on Nov. 8, 2020, 6:26 p.m.