PomaVolcano: Volcano Plot

In pcastellanoescuder/POMA_package: Tools for Omics Data Analysis

Volcano Plot

Description

PomaVolcano creates a volcano plot from a given dataset. This function is designed to visualize the statistical significance (p-value) against the magnitude of change (log2 fold change) for features.

Usage

PomaVolcano(
  data,
  pval_cutoff = 0.05,
  log2fc_cutoff = NULL,
  labels = FALSE,
  x_label = "log2 (Fold Change)",
  y_label = "-log10 (P-value)"
)

Arguments

data	A data frame with at least three columns: feature names, effect size (e.g., logFC), and statistical significance values. These should be the first three columns of the data, in this order.
pval_cutoff	Numeric. Specifies the p-value threshold for significance in the volcano plot. The default is set to 0.05. This parameter determines the horizontal line in the plot indicating the threshold for statistical significance.
log2fc_cutoff	Numeric. Specifies the log2 fold change cutoff for the volcano plot. If not provided, the cutoff is set to the 75th percentile of the absolute log2 fold changes in the data. This parameter determines the vertical lines in the plot indicating the magnitude of change threshold.
labels	Logical. Indicates whether to plot labels for significant features.
x_label	Character. Custom label for the x-axis.
y_label	Character. Custom label for the y-axis.

Value

A ggplot object representing the volcano plot.

Author(s)

Pol Castellano-Escuder

Examples

data <- POMA::st000336 # Example SummarizedExperiment object included in POMA

# T-test
results <- data %>%
  PomaImpute() %>% 
  PomaUnivariate() %>% 
  dplyr::select(feature, fold_change, pvalue)

results %>% 
  PomaVolcano(pval_cutoff = 0.05,
              log2fc_cutoff = NULL,
              labels = FALSE,
              x_label = "log2 (Fold Change)",
              y_label = "-log10 (P-value)")
              
# Limma
results <- data %>%
  PomaImpute() %>% 
  PomaNorm() %>% 
  PomaLimma(contrast = "DMD-Controls") %>% 
  dplyr::select(feature, log2FC, pvalue)

results %>% 
  PomaVolcano(pval_cutoff = 0.05,
              log2fc_cutoff = NULL,
              labels = FALSE,
              x_label = "log2 (Fold Change)",
              y_label = "-log10 (P-value)")

pcastellanoescuder/POMA_package documentation built on Oct. 13, 2024, 8:47 p.m.