Move advanced flip examples to separate vignette

R/flip.R

@@ -4,6 +4,9 @@
 #' sequences and their features. `sync` automatically flips bins using a
 #' heuristic that maximizes the amount of forward strand links between
 #' neighboring bins.
+#' 
+#' For more details see the help vignette:
+#' \code{vignette("flip", package = "gggenomes")}
 #'
 #' @param x a gggenomes object
 #' @param ... bins or sequences to flip in dplyr::select like syntax (numeric
@@ -45,38 +48,6 @@
 #'   sync() + labs(caption="shared orthologs")
 #'
 #' 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"))
-#'
-#' 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", 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")
 #' @export
 flip <- function(x, ..., .bin_track=seqs){
   UseMethod("flip")

vignettes/flip.Rmd

@@ -0,0 +1,80 @@
+---
+title: "Advanced flip examples"
+author: "Thomas Hackl"
+date: "`r format(Sys.Date())`"
+vignette: >
+  %\VignetteIndexEntry{Flip}
+  %\VignetteEngine{knitr::rmarkdown}
+  %\VignetteEncoding{UTF-8}
+---
+
+``` {r}
+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")
+```