PlotVolcano

Plot volcano plot from a geneda object. Requires that you have ran SetDEGs on your object following differential expression in DESeq2.

Usage

PlotVolcano(object, assay, alpha, l2fc, den = NULL, num = NULL, title = NULL)

Arguments

object

A geneda object containing DEGs from SetDEGs method

assay

The DEG slot to use for visualization

alpha

Threshold for adjusted p-values (padj column from DESeq2)

l2fc

Absolute value log2Fold-change magnitude threshold (log2FoldChange column)

den

Denominator (reference level for comparison, num vs. den). If NULL, the legend uses "denominator".

num

Numerator (numerator level for comparison, num vs. den). If NULL, the legend uses "numerator".

title

Optional character vector of what plot should be titled.

Value

A ggplot2 object

Details

Thresholds are inclusive (padj <= alpha, |log2FoldChange| >= l2fc), matching FilterDEGs(). Genes with a missing log2FoldChange or padj are not plotted.

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")
PlotVolcano(obj,
    assay = "KO_vs_WT", alpha = 0.05, l2fc = 1,
    den = "WT", num = "Snai1_KO"
)