Introduction to ‘gggenes’

David Wilkins

2017-08-24

‘gggenes’ is a (quite small) set of tools for drawing gene arrow maps with ‘ggplot2.’

geom_gene_arrow

geom_gene_arrow is a ‘ggplot2’ geom that represents genes with arrows. The start and end positions of the genes within their molecule(s) are mapped to the xmin and xmax aesthetics respectively. The y aesthetic must be mapped to the molecule(s). If you are drawing more than one molecule, and the numerical positions of the genes are not similar across molecules, you almost certainly want to facet the plot with scales = "free" to avoid drawing ridiculously large molecules with ridiculously tiny genes.

library(ggplot2)
library(gggenes)

ggplot2::ggplot(example_genes, ggplot2::aes(xmin = start, xmax = end, y =
                                            molecule, fill = gene)) +
  geom_gene_arrow() +
  ggplot2::facet_wrap(~ molecule, scales = "free", ncol = 1) +
  ggplot2::scale_fill_brewer(palette = "Set3")

theme_genes

Because the resulting plot can look cluttered, a ‘ggplot2’ theme theme_genes is provided with some sensible defaults.

ggplot2::ggplot(example_genes, ggplot2::aes(xmin = start, xmax = end, y =
                                            molecule, fill = gene)) +
  geom_gene_arrow() +
  ggplot2::facet_wrap(~ molecule, scales = "free", ncol = 1) +
  ggplot2::scale_fill_brewer(palette = "Set3") +
  theme_genes()

make_alignment_dummies

Often you might want to a certain gene to be vertically aligned across the faceted molecules. A helper function make_alignment_dummies is provided that generates a set of ‘dummy’ genes such that, if the dummies are added to the plot with geom_blank, they will extend the range of each facet to visually align the selected gene across facets.

dummies <- make_alignment_dummies(
  example_genes,
  ggplot2::aes(xmin = start, xmax = end, y = molecule, id = gene),
  on = "genE"
)

ggplot2::ggplot(example_genes, ggplot2::aes(xmin = start, xmax = end, y =
                                            molecule, fill = gene)) +
  geom_gene_arrow() +
  ggplot2::geom_blank(data = dummies) +
  ggplot2::facet_wrap(~ molecule, scales = "free", ncol = 1) +
  ggplot2::scale_fill_brewer(palette = "Set3") +
  theme_genes()