Interactive plots with plotly

Every ggvariant plot function accepts interactive = TRUE, which routes the plot through plotly instead of returning a static ggplot object. This is useful for sharing a plot with collaborators who don’t use R: a plotly widget can be saved as a standalone HTML file and opened in any browser.

plotly is a Suggests dependency, not a hard dependency of ggvariant – the chunks on this page only run when plotly is installed on the machine building the site.

library(ggvariant)

vcf_file <- system.file("extdata", "example.vcf", package = "ggvariant")
variants <- read_vcf(vcf_file)
#> ℹ Reading VCF: example.vcf
#> ✔ Reading VCF: example.vcf [20ms]
#> 
#> Loaded 19 variant records across 7 chromosomes.

Interactive lollipop plot

Hovering over a point shows the position, amino-acid change, consequence, and sample.

plot_lollipop(variants, gene = "TP53", interactive = TRUE)

Interactive oncoprint

plot_oncoprint(variants, top_n = 6, interactive = TRUE)

Saving a widget for sharing

p <- plot_lollipop(variants, gene = "TP53", interactive = TRUE)
htmlwidgets::saveWidget(p, "TP53_lollipop.html")

htmlwidgets::saveWidget() is not a formal dependency of ggvariant – install it separately (install.packages("htmlwidgets")) if you want to export a standalone file this way.