volcano_plot: Volcano plot

In compbiomed/BatchQC: Batch Effects Quality Control Software

Volcano plot

Description

This function allows you to plot DE analysis results as a volcano plot

Usage

volcano_plot(DE_results, pslider = 0.05, fcslider)

Arguments

DE_results	a dataframe with the results of one of the DE Analysis; must include "log2FoldChange" and "pvalue" columns
pslider	Magnitude of significance value threshold, default is 0.05
fcslider	Magnitude of expression change value threshold

Value

A volcano plot of expression change and significance value data

Examples

library(scran)
se <- mockSCE()
differential_expression <- BatchQC::DE_analyze(se = se,
                                                method = "DESeq2",
                                                batch = "Treatment",
                                                conditions = c(
                                                "Mutation_Status",
                                                "Cell_Cycle"),
                                                assay_to_analyze = "counts")
value <- round((max(abs(
    differential_expression[[length(differential_expression)]][, 1]))
    + min(abs(
    differential_expression[[length(differential_expression)]][, 1]))) / 2)

volcano_plot(differential_expression[[1]], pslider = 0.05, fcslider = value)

compbiomed/BatchQC documentation built on Nov. 16, 2024, 5:47 a.m.