align: Align genomes relative to target genes, feats, seqs, etc.

In gggenomes: A Grammar of Graphics for Comparative Genomics

Align genomes relative to target genes, feats, seqs, etc.

Description

Align your genomes relative to target features, such as genes or regions of interest. Use the ... argument to indicate a subset of features in one track as targets. If multiple features are selected per bin, they are treated as a single feature spanning from the leftmost to the rightmost end. The genomes will be shifted so that the targets features align according to the .justify.

Usage

align(x, ..., .track_id = "genes", .justify = "left")

Arguments

x	gggenomes object
...	filter expression to identify target features in target track. Works like dplyr::filter() <data-masking>.
.track_id	track to pull from, default "genes"
.justify	alignment position, one of "left", "center", "right" or numeric between 0 and 1, default "left"

Value

gggenomes object with shifted coordinates.

Examples

library(patchwork)
p <- gggenomes(emale_genes, links = emale_ava) +
  geom_link() +
  geom_gene(aes(fill = name)) +
  scale_fill_brewer(palette = "Dark2", na.value = "cornsilk3") +
  geom_bin_label()

pp <-
  # left-align on MCP gene
  p |> align(name == "MCP") +
  # right-align on MCP gene
  p |> align(name == "MCP", .justify = "right") +
  # center-align on MCP + pri-hel gene after flipping bins
  p |> sync() |> align(name %in% c("MCP", "pri-hel"), .justify = "center") |>
    # and highlight the feature block we are aligning to
    locate(name %in% c("MCP", "pri-hel"), .expand = 0, .max_dist = 1e6) +
    geom_feat(data = feats(loci), color = "plum3", alpha = .5, linewidth = 5)

pp + plot_layout(guides = "collect") & geom_vline(xintercept = 0, linetype = 2)

# multi contig
s0 <- tibble::tibble(
  bin_id = c("A", "B", "B", "B", "C", "C", "C"),
  seq_id = c("a1", "b1", "b2", "b3", "c1", "c2", "c3"),
  length = c(1e4, 6e3, 2e3, 1e3, 3e3, 3e3, 3e3)
)

p <- gggenomes(seqs = s0) +
  geom_seq(aes(color = bin_id), linewidth = 3) +
  geom_bin_label() +
  geom_seq_label() +
  expand_limits(color = c("A", "B", "C"))

pp <-
  # center on everything - just omit ...
  p |> align(.track_id = "seqs", .justify = .5) +
  # right-align on contig ending in "2"
  # NOTE: there is no 2nd contig in bin A, so nothing is aligned there
  p |> align(stringr::str_detect(seq_id, "2"), .track_id = "seqs", .justify = "right")

pp + plot_layout(guides = "collect") & geom_vline(xintercept = 0, linetype = 2)

gggenomes documentation built on Nov. 14, 2025, 5:07 p.m.