Merge pull request #162 from thackl/geom_seq_break

added geom_seq_break()

NAMESPACE

@@ -123,6 +123,7 @@ export(geom_gene_tag)
 export(geom_gene_text)
 export(geom_link)
 export(geom_seq)
+export(geom_seq_break)
 export(geom_seq_label)
 export(geom_variant)
 export(geom_wiggle)
@@ -189,6 +190,7 @@ import(grid)
 import(purrr)
 import(rlang)
 importFrom(ggplot2,geom_segment)
+importFrom(ggplot2,geom_text)
 importFrom(ggplot2,theme)
 importFrom(ggplot2,theme_bw)
 importFrom(jsonlite,fromJSON)

R/geom_seq_break.R

@@ -0,0 +1,74 @@
+#' Decorate truncated sequences
+#'
+#' @description
+#' `geom_seq_break()` adds decorations to the ends of truncated sequences. These
+#' could arise from zooming onto sequence loci with `focus()`, or manually
+#' annotating sequences with start > 1 and/or end < length.
+#' @param label the character to decorate ends with. Provide two values for
+#' different start and end decorations, e.g. `label=c("]", "[")`.
+#' @param data_start seq_layout of sequences for which to decorate the start.
+#' default: `seqs(start >1)`
+#' @param data_end seq_layout of sequences for which to decorate the end.
+#' default: `seqs(end < length)`
+#' @inheritParams ggplot2::geom_text
+#' @importFrom ggplot2 geom_text
+#' @export
+#' @examples
+#' # decorate breaks created with focus()
+#' gggenomes(emale_genes, emale_seqs) |>
+#'   focus(.expand=1e3, .max_dist = 1e3) +
+#'   geom_seq() + geom_gene() +
+#'   geom_seq_break()
+#'
+#' # customize decorations
+#' gggenomes(emale_genes, emale_seqs) |>
+#'   focus(.expand=1e3, .max_dist = 1e3) +
+#'   geom_seq() + geom_gene() +
+#'   geom_seq_break(label=c("[", "]"), size=3, color="#1b9e77")
+#'
+#' # decorate manually truncated sequences
+#' s0 <- tribble(
+#'   # start/end define regions, i.e. truncated contigs
+#'   ~bin_id, ~seq_id, ~length, ~start, ~end,
+#'   "complete_genome", "chromosome_1_long_trunc_2side", 1e5, 1e4, 2.1e4,
+#'   "fragmented_assembly", "contig_1_trunc_1side", 1.3e4, .9e4, 1.3e4,
+#'   "fragmented_assembly", "contig_2_short_complete", 0.3e4, 1, 0.3e4,
+#'   "fragmented_assembly", "contig_3_trunc_2sides", 2e4, 1e4, 1.4e4
+#' )
+#'
+#' l0 <- tribble(
+#'   ~seq_id, ~start, ~end, ~seq_id2, ~start2, ~end2,
+#'   "chromosome_1_long_trunc_2side", 1.1e4, 1.4e4,
+#'   "contig_1_trunc_1side", 1e4, 1.3e4,
+#'   "chromosome_1_long_trunc_2side", 1.4e4, 1.7e4,
+#'   "contig_2_short_complete", 1, 0.3e4,
+#'   "chromosome_1_long_trunc_2side", 1.7e4, 2e4,
+#'   "contig_3_trunc_2sides", 1e4, 1.3e4
+#' )
+#'
+#' gggenomes(seqs=s0, links=l0) +
+#'   geom_seq() + geom_link() +
+#'   geom_seq_label(nudge_y=-.05) +
+#'   geom_seq_break()
+geom_seq_break <- function(mapping_start = NULL, mapping_end = NULL,
+                       data_start = seqs(start > 1), data_end=seqs(end < length),
+                       label="/", size=4, hjust=.75, family="bold", stat="identity",
+                       na.rm = FALSE, show.legend = NA, inherit.aes = TRUE, ...){
+
+  label_start <- label[1]
+  label_end <- label[length(label)]
+
+  aes_start <- aes(x=x, y=y)
+  aes_start <- gggenomes:::aes_intersect(mapping_start, aes_start)
+
+  aes_end <- aes(x=xend, y=y)
+  aes_end <- gggenomes:::aes_intersect(mapping_end, aes_end)
+
+  list(
+    geom_text(aes_start, data=data_start, label=label_start, size=size, hjust=hjust,
+              family=family, ...),
+    geom_text(aes_end, data=data_end, label=label_end, size=size, hjust=1-hjust,
+              family=family, ...)
+  )
+}
+