plot_volcano-ReactomeAnalysisResult-method: ReactomeAnalysisResult - plot_volcano

In ReactomeGSA: Client for the Reactome Analysis Service for comparative multi-omics gene set analysis

Description

Creates a volcano plot for the pathway analysis result. Every point represents one pathway, the x-axis the log fold-change and the y-axis the adjusted p-value (-log10).

Usage

## S4 method for signature 'ReactomeAnalysisResult'
plot_volcano(x, dataset = 1, ...)

Arguments

x	ReactomeAnalysisResult. The analysis result to plot the volcano plot for.
dataset	The name or index of the dataset to plot (first one by default).
...	Additional parameters for specific implementations.

Details

This function is only available for GSA-based analysis results.

Value

A ggplot2 plot object representing the volcano plot.

See Also

Other ReactomeAnalysisResult functions: get_result(), names,ReactomeAnalysisResult-method, open_reactome(), pathways(), plot_correlations(), plot_gsva_heatmap(), plot_gsva_pathway(), reactome_links(), result_types()

Examples

# load an example result
library(ReactomeGSA.data)
data(griss_melanoma_result)

# create the volcano plot for the first dataset
plot_obj <- plot_volcano(griss_melanoma_result)

# display the plot using `print(plot_obj)`

Example output

Loading required package: limma
Loading required package: edgeR
Loading required package: Seurat

ReactomeGSA documentation built on April 17, 2021, 6:01 p.m.