Plotting subsets of sequences

[npcooley]

I can't seem to find any examples that describe how to do the task that i'm interested in, so I'm just creating this issue:

If i have a scenario where i have two genomes that are both 6M bp long, and I want to plot region subsets against each other, i.e. 300k-350k in genome 1, and 1.5M-1.55M in genome 2. How do i use this package to plot this kind of comparison?

[thackl]

Hi Nicholas,

you can zoom in on explicit subsets, either by adding a start and end column the sequence table for gggenomes(seqs=...) or by given a dataframe with seq_id, start, end to focus(.loci=...).

With focus you can also dynamically zoom in on regions, e.g. by specifying a selector for features. Something like focus(.track_id=genes, str_detect(name, "dnaB") ) will give all regions around "dnaB" genes. Or focus(.track_id=links) will zoom in on all regions that share similarity with other genomes.

Does that answer you question?

library(tidyverse)
library(gggenomes)

# Two 6Mbp genomes with one chromosome each
seqs = tibble(
  seq_id = c("A", "B"),
  bin_id = seq_id,
  length = 6e6)

# some links between different parts of genomes
links = tibble(
  seq_id = "A",
  start = 1e5,
  end = 1.1e5,
  seq_id2 = "B",
  start2 = 3e5,
  end2=3.15e5)

# full genomes, no zoom
p1 <- gggenomes(seqs=seqs, links=links) +
  geom_seq() +
  geom_seq_label() +
  geom_link()
 
# zoom in by added start/end to sequence track
seqs_start_end <- seqs |>
  mutate(start = c(0.8e5, 2.8e5), end = c(1.3e5, 3.3e5))
p2 <- gggenomes(seqs=seqs_start_end, links=links) +
  geom_seq() +
  geom_seq_label() +
  geom_link()

# zoom in by focus(.loci=)
p3 <- gggenomes(seqs=seqs, links=links) |> 
  focus(.loci=tibble(seq_id = c("A", "B"), start=c(0.8e5, 2.8e5), end = c(1.3e5, 3.3e5))) +
  geom_seq() +
  geom_seq_label() +
  geom_link()

# zoom in dynamically with focus()
p4 <- gggenomes(seqs=seqs, links=links) |> 
  focus(
    .track_id=links, # zoom in on any links
    .locus_id = str_glue("{seq_id}:{start}-{end}") # add start/end to contig name
  ) +
  geom_seq() +
  geom_link() +
  geom_seq_label()


library(patchwork)

p1 + p2 + p3 + p4