gggenes is a ggplot2 extension for drawing gene arrow maps.
Install the stable 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() is a ggplot2 geom that represents genes with arrows.
The start and end locations of the genes within their molecule(s) are
mapped to the xmin and xmax aesthetics respectively. These start and
end locations are used to determine the directions in which the arrows
point. The y aesthetic must be mapped to the molecule(s). If you are
drawing more than one molecule, and the numerical locations 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)
ggplot(example_genes, aes(xmin = start, xmax = end, y = molecule, fill = gene)) +
geom_gene_arrow() +
facet_wrap(~ molecule, scales = "free", ncol = 1) +
scale_fill_brewer(palette = "Set3")Because the resulting plot can look cluttered, a ggplot2 theme
theme_genes is provided with some sensible
defaults.
ggplot(example_genes, aes(xmin = start, xmax = end, y = molecule, fill = gene)) +
geom_gene_arrow() +
facet_wrap(~ molecule, scales = "free", ncol = 1) +
scale_fill_brewer(palette = "Set3") +
theme_genes()Often you will want a certain gene to be vertically aligned across the
faceted molecules. make_alignment_dummies() generates a set of dummy
genes that if added to the plot with geom_blank() will extend the
range of each facet to visually align the selected gene across facets.
dummies <- make_alignment_dummies(
example_genes,
aes(xmin = start, xmax = end, y = molecule, id = gene),
on = "genE"
)
ggplot(example_genes, aes(xmin = start, xmax = end, y = molecule, fill = gene)) +
geom_gene_arrow() +
geom_blank(data = dummies) +
facet_wrap(~ molecule, scales = "free", ncol = 1) +
scale_fill_brewer(palette = "Set3") +
theme_genes()To label individual genes, provide a label aesthetic and use
geom_gene_label(). geom_gene_label() uses the
ggfittext package to fit the
label text inside the gene arrows; see the ggfittext documentation for
more details on how it resizes and reflows text to make it fit.
ggplot(
example_genes,
aes(xmin = start, xmax = end, y = molecule, fill = gene, label = gene)
) +
geom_gene_arrow(arrowhead_height = unit(3, "mm"), arrowhead_width = unit(1, "mm")) +
geom_gene_label(align = "left") +
geom_blank(data = dummies) +
facet_wrap(~ molecule, scales = "free", ncol = 1) +
scale_fill_brewer(palette = "Set3") +
theme_genes()Sometimes you might want to reverse the direction of some genes from
that implied by xmin and xmax. For example, you might want to draw
both a forward and reverse strand within each facet, and reverse the
direction of all the genes on the reverse strand. The optional forward
aesthetic is intended for this sort of situation.
If forward is TRUE (the default), or any value that coerces to TRUE
such as 1, the gene will be drawn pointing in the normal direction,
i.e. that implied by xmin and xmax. If forward is FALSE, or any
value that coerces to FALSE such as -1, the gene will be drawn in the
reverse of this implied direction. In the following example, the
forward aesthetic has been used to reverse the direction of all genes
on the reverse strand from that implied by xmin and
xmax.
example_genes$direction <- ifelse(example_genes
766B
$strand == "forward", 1, -1)
ggplot(subset(example_genes, molecule == "Genome1"),
aes(xmin = start, xmax = end, y = strand, fill = gene,
forward = direction)) +
geom_gene_arrow() +
theme_genes()We can highlight subgene segments, such as protein domains or local
alignments, using geom_subgene_arrow().
This works similarly to geom_gene_arrow(), but in addition to xmin
and xmax (which determine the gene boundaries), we need the aesthetics
xsubmin and xsubmax to determine the subgene boundaries.
geom_gene_arrow() will produce pretty arrowheads, as long as xmin >= xsubmin and xmax >= xsubmax for all subgenes (subgenes that break
gene boundaries will be skipped with a warning).
The suggested usage is to use geom_gene_arrow() with no fill, and then
add a subgene layer over this:
ggplot(example_genes, aes(xmin = start, xmax = end, y = molecule)) +
facet_wrap(~ molecule, scales = "free", ncol = 1) +
geom_gene_arrow(fill = "white") +
geom_subgene_arrow(data = example_subgenes,
aes(xmin = start, xmax = end, y = molecule, fill = gene,
xsubmin = from, xsubmax = to), color="black", alpha=.7) +
theme_genes()To label subgenes, we can use geom_subgene_label(), which works
similarly to geom_gene_label() with the major difference that it
requires xsubmin and xsubmax aesthetics (not xmin and xmax).
ggplot(subset(example_genes, molecule == "Genome4" & gene == "genA"),
aes(xmin = start, xmax = end, y = strand)
) +
geom_gene_arrow() +
geom_gene_label(aes(label = gene)) +
geom_subgene_arrow(
data = subset(example_subgenes, molecule == "Genome4" & gene == "genA"),
aes(xsubmin = from, xsubmax = to, fill = subgene)
) +
geom_subgene_label(
data = subset(example_subgenes, molecule == "Genome4" & gene == "genA"),
aes(xsubmin = from, xsubmax = to, label = subgene),
min.size = 0
)