knitr::opts_chunk$set( collapse = TRUE, comment = "#>", fig.path = "man/figures/README-" )
'gggenes' is a (quite small) set of tools for drawing gene arrow maps with 'ggplot2.'
Install the release version of 'gggenes' from CRAN:
install.packages("gggenes")
If you want the development version, install it from GitHub:
devtools::install_github("wilkox/gggenes")
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 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()
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