Hi, I am comparing circular sequences with random start points. It there a way tha

Not 100% sure what you mean, but could this be it <a href="https://thackl.github.io/gg

Changing start site of seq track and keeping layout. about gggenomes HOT 4 OPEN

Rikkiff commented on July 20, 2024

Changing start site of seq track and keeping layout.

from gggenomes.

Comments (4)

thackl commented on July 20, 2024

Not 100% sure what you mean, but could this be it https://thackl.github.io/gggenomes/reference/shift.html

from gggenomes.

Rikkiff commented on July 20, 2024

Thanks Thomas!
Actually, I want to change the start site of the sequences. So, for example that all sequences are starting with the MCP gene you are centring on in your example.

from gggenomes.

thackl commented on July 20, 2024

Ah, ok, so you sort of want to rotate the annotations. How about something like this:

library(tidyverse)
library(gggenomes)

s1 <- tibble(
  seq_id = c("A", "B"),
  length = 2000
)

g1 <- tibble(
  seq_id = rep(c("A", "B"), each=4),
  feat_id = c("a-start", "a2", "a3", "a4", "b3", "b4", "b-start", "b2"),
  start = rep(c(100, 600, 1100, 1600), 2),
  end = start +300)

Original sequence with B having start in the middle

#| fig.height: 2
#| fig.width: 5
gggenomes(g1, s1) +
  geom_seq() +
  geom_gene() +
  geom_gene_tag(aes(label=feat_id))

B broken up at start gene and first half of genome plotted as individual contig before second half of genome

#| fig.height: 2
#| fig.width: 5
# "zoom" in on parts of sequences and reorganize
# use all of A:0-2000, use B:1000-2000, then B:0:1000
p1 <- gggenomes(g1, s1, spacing = 10) |> # spacing controls the distance between contigs of same genome
  focus(.loci = tibble(  
    seq_id = c("A", "B", "B"),
    start = c(0, 1000, 0),
    end = c(2000, 2000, 1000)))
p1 + 
  geom_seq() +
  geom_gene() +
  geom_gene_tag(aes(label=feat_id))