# Advanced flip examples

#### Thomas Hackl

#### 2025-11-13

    library(gggenomes)

    ## Loading required package: ggplot2

    ## gggenomes v1.1.2
    ##
    ## If you use 'gggenomes' in published research, please cite:
    ##
    ## Hackl T, Ankenbrand M, van Adrichem B, Wilkins D, Haslinger K (2024).
    ## "gggenomes: effective and versatile visualizations for comparative
    ## genomics." _arXiv_. doi:10.48550/arXiv.2411.13556
    ## <https://doi.org/10.48550/arXiv.2411.13556>.

    ##
    ## Attaching package: 'gggenomes'

    ## The following object is masked from 'package:graphics':
    ##
    ##     layout

    library(patchwork)

    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")

    ## No seqs provided, inferring seqs from feats

    # 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")

    ## Flipping: E4-10_086,E4-10_112,RCC970_016B

    # flip automatically based on protein-protein links
    p3 <- p %>% add_sublinks(emale_prot_ava) %>%
      sync() + labs(caption="protein alignments")

    ## Transforming sublinks with "aa2nuc". Disable with `.transform = "none"`
    ## Flipping: E4-10_086,E4-10_112,RCC970_016B

    # 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")

    ## Joining with `by = join_by(feat_id)`
    ## Flipping: E4-10_086,E4-10_112,RCC970_016B

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

    # 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"))

    ## Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
    ## ℹ Please use `linewidth` instead.
    ## ℹ The deprecated feature was likely used in the gggenomes package.
    ##   Please report the issue at <https://github.com/thackl/gggenomes/issues>.
    ## This warning is displayed once every 8 hours.
    ## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
    ## generated.

    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")

    # fancy flipping using tidyselect::where for dynamic selection
    p <- gggenomes(emale_genes,emale_seqs) %>% add_clusters(emale_cogs) +
      geom_seq(color="grey70", linewidth=1, arrow = arrow(angle = 30, length = unit(15, "pt"),
        ends = "last", type = "open")) +
      geom_gene(aes(fill=cluster_id))

    ## Joining with `by = join_by(feat_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")