do_VolcanoPlot() | DE volcano plots

Volcano plots display differential expression results showing both fold change (X-axis) and statistical significance (Y-axis). Points are colored by significance category with optional gene labels.

Basic usage

First run differential expression:

de_genes <- Seurat::FindMarkers(sample, ident.1 = "IPC-like", ident.2 = "Cilia-like")

p <- SCpubr::do_VolcanoPlot(sample = sample,
                            de_genes = de_genes)
p

Adjust cutoffs

p <- SCpubr::do_VolcanoPlot(sample = sample,
                            de_genes = de_genes,
                            pval_cutoff = 0.01,
                            FC_cutoff = 1.5)
p

Control gene labels

# Show more genes
p <- SCpubr::do_VolcanoPlot(sample = sample,
                            de_genes = de_genes,
                            n_genes = 10)
p

Disable gene labels

p <- SCpubr::do_VolcanoPlot(sample = sample,
                            de_genes = de_genes,
                            add_gene_tags = FALSE)
p

Order labels by significance or fold change

# By p-value
p <- SCpubr::do_VolcanoPlot(sample = sample,
                            de_genes = de_genes,
                            order_tags_by = "pvalue")
p

# By log fold change
p <- SCpubr::do_VolcanoPlot(sample = sample,
                            de_genes = de_genes,
                            order_tags_by = "logfc")
p

Use labels instead of text

p <- SCpubr::do_VolcanoPlot(sample = sample,
                            de_genes = de_genes,
                            use_labels = TRUE)
p

Hide threshold lines

p <- SCpubr::do_VolcanoPlot(sample = sample,
                            de_genes = de_genes,
                            plot_lines = FALSE)
p

Parameter reference

Note

For parameters shared across many functions (color palettes, typography, legend styling), see Shared features.

Core parameters

Parameter Description Default
de_genes Output from FindMarkers() —
pval_cutoff P-value threshold 0.05
FC_cutoff Fold change threshold 2

Gene labeling

Parameter Description Default
add_gene_tags Show gene labels TRUE
n_genes Number of genes to label 5
add_tag_side "both", "positive", "negative" "both"
order_tags_by "both", "pvalue", "logfc" "both"
use_labels Use geom_label() FALSE
tag_size Label text size 6

Threshold lines

Parameter Description Default
plot_lines Show threshold lines TRUE
line_color Line color "grey75"
line_size Line thickness 0.5

See also