PomaVolcano {POMA} | R Documentation

## Volcano Plot

### 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()

[Package POMA version 1.2.0 Index]