PlotPValHist

Generate a p-value histogram from a DEG table inside a geneda object. This function uses raw p-values only and highlights p-values below a given threshold (default 0.05).

Usage

PlotPValHist(object, assay, bins = 40, alpha = 0.05, title = NULL)

Arguments

object

A geneda object containing DEGs in the DEGs slot.

assay

The name of the DEG table to use (must contain a "pvalue" column).

bins

Number of histogram bins (default 40).

alpha

Significance threshold (default 0.05). Bars representing p-values < alpha will be highlighted.

title

Optional title for the plot.

Value

A ggplot2 object

Examples

data(Snail1KO)
counts <- as.matrix(Snail1KO$rawCounts)
counts <- counts[rowSums(counts >= 10) >= 3, ]
meta <- Snail1KO$metadata
rownames(meta) <- meta$Sample
meta$Genotype <- factor(meta$Genotype, levels = c("WT", "Snai1_KO"))
norm <- log2(t(t(counts) / colSums(counts)) * 1e6 + 1)
obj <- GenEDA(normalized = norm, metadata = meta, counts = counts)

# Differential expression with DESeq2 (Snai1_KO vs WT)
dds <- DESeq2::DESeqDataSetFromMatrix(counts, meta, design = ~Genotype)
dds <- DESeq2::DESeq(dds, quiet = TRUE)
res <- as.data.frame(DESeq2::results(dds))
obj <- SetDEGs(obj, res, assay = "KO_vs_WT")
PlotPValHist(obj, assay = "KO_vs_WT")