plot_volcano: 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

plot_volcano(x, ...)

Arguments

x	ReactomeAnalysisResult. The analysis result to plot the volcano plot for.
...	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.