Advanced flip examples

In gggenomes: A Grammar of Graphics for Comparative Genomics

library(gggenomes)
library(patchwork)

``` {r dpi=36, out.width="720px"} p <- gggenomes(genes=emale_genes) + geom_seq(aes(color=strand), arrow=TRUE) + geom_link(aes(fill=strand)) + expand_limits(color=c("-")) + labs(caption="not flipped")

nothing flipped

p0 <- p %>% add_links(emale_ava)

flip manually

p1 <- p %>% add_links(emale_ava) %>% flip(4:6) + labs(caption="manually")

flip automatically based on genome-genome links

p2 <- p %>% add_links(emale_ava) %>% sync() + labs(caption="genome alignments")

flip automatically based on protein-protein links

p3 <- p %>% add_sublinks(emale_prot_ava) %>% sync() + labs(caption="protein alignments")

flip automatically based on genes linked implicitly by belonging

to the same clusters of orthologs (or any grouping of your choice)

p4 <- p %>% add_clusters(emale_cogs) %>% sync() + labs(caption="shared orthologs")

p0 + p1 + p2 + p3 + p4 + plot_layout(nrow=1, guides="collect")

``` {r dpi=36, out.width="720px"}
# flip seqs inside bins
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), size=1, arrow = arrow(angle = 30, length = unit(10, "pt"),
    ends = "last", type = "open")) +
  geom_bin_label() + geom_seq_label() +
  expand_limits(color=c("A","B","C"))

p1 <- p %>% flip_seqs(6)
p2 <- p %>% flip_seqs(c2)
p3 <- p %>% flip_seqs(2, .bins = C)

p + p1 + p2 + p3 + plot_layout(nrow=1, guides="collect")

``` {r dpi=36, out.width="720px"}

fancy flipping using tidyselect::where for dynamic selection

p <- gggenomes(emale_genes,emale_seqs) %>% add_clusters(emale_cogs) + geom_seq(color="grey70", size=1, arrow = arrow(angle = 30, length = unit(15, "pt"), ends = "last", type = "open")) + geom_gene(aes(fill=cluster_id))

flip all short seqs - where() applied to .bin_track=seqs

p1 <- p %>% flip(where(~.x$length < 21000))

flip all seqs with MCP on "-" - where() applied to .bin_track=genes

p2 <- p %>% flip(where(~any(.x$strand[.x$cluster_id %in% "cog-MCP"] == "-")), .bin_track=genes)

p + p1 + p2 + plot_layout(nrow=1, guides="collect") & theme(legend.position = "bottom") ```

gggenomes documentation built on Sept. 11, 2024, 8:55 p.m.