Package index • ggvariant

Package overview

ggvariant-package ggvariant: ggvariant: Tidy, ggplot2-Native Visualization for Genomic Variants

Reading and coercing variants

Get variant data into the tidy gvf format every ggvariant plot function accepts.

read_vcf(): Read a VCF file into a tidy variant data frame
coerce_variants(): Coerce a plain data frame to a gvf object
print(<gvf>) summary(<gvf>) print(<summary.gvf>): Print and summarise gvf objects

Plots

ggplot2-native plotting functions, one per visualisation type.

plot_lollipop(): Lollipop plot of variants along a gene
plot_consequence_summary(): Consequence summary bar chart
plot_variant_spectrum(): Mutational spectrum (SBS) bar chart
plot_oncoprint() plot_waterfall(): Oncoprint / waterfall plot of variants across samples
plot_tmb(): Tumour mutational burden bar chart

Palettes and themes

Built-in colour palettes and the shared plot theme, exported for reuse when customising a plot’s ggplot2 layers directly.

gv_palette(): ggvariant colour palettes
theme_ggvariant(): ggvariant ggplot2 theme