PlotVolcano

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

PlotVolcano(object, assay, alpha, l2fc, den, num, 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)

num

Numerator (numerator level for comparison, num vs. den)

title

Optional character vector of what plot should be titled.

Value

A ggplot2 object

Examples

# \donttest{
mock_norm <- matrix(rnorm(5000 * 6, mean = 0, sd = 2), nrow = 5000, ncol = 6)
colnames(mock_norm) <- paste0("Sample", 1:6)
rownames(mock_norm) <- paste0("Gene", 1:5000)

# Sample metadata
mock_meta <- data.frame(condition = c("A","B","A","B","A","B"),
row.names = colnames(mock_norm))

# Construct GenEDA object
obj <- GenEDA(normalized = mock_norm, metadata = mock_meta)

# make dummy DEG table
n <- 1000
genes <- paste0("Gene", 1:n)
log2FoldChange <- runif(n, min = -5, max = 5)
padj <- runif(n, min = 0, max = 1)
df <- data.frame(
 log2FoldChange = log2FoldChange,
 padj = padj,
 stringsAsFactors = FALSE)
rownames(df) <- genes
obj <- SetDEGs(obj, df, "DEGs")

PlotVolcano(obj, "DEGs", 0.05, 1, "Denominator Group", "Numerator Group", "Test")
#> Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
#> ℹ Please use `linewidth` instead.
#> ℹ The deprecated feature was likely used in the RGenEDA package.
#>   Please report the issue to the authors.
#> Warning: ggrepel: 13 unlabeled data points (too many overlaps). Consider increasing max.overlaps
#> Warning: ggrepel: 3 unlabeled data points (too many overlaps). Consider increasing max.overlaps

# }