From 58335ca48e04e748eb2e5f5c6734ed708d4512ef Mon Sep 17 00:00:00 2001
From: Thomas Hackl <thackl@lim4.de>
Date: Thu, 12 Oct 2023 23:59:16 +0200
Subject: [PATCH] forgot man/geom_seq_break

---
 man/geom_seq_break.Rd | 99 +++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 99 insertions(+)
 create mode 100644 man/geom_seq_break.Rd

diff --git a/man/geom_seq_break.Rd b/man/geom_seq_break.Rd
new file mode 100644
index 0000000..8cd9344
--- /dev/null
+++ b/man/geom_seq_break.Rd
@@ -0,0 +1,99 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/geom_seq_break.R
+\name{geom_seq_break}
+\alias{geom_seq_break}
+\title{Decorate truncated sequences}
+\usage{
+geom_seq_break(
+  mapping_start = NULL,
+  mapping_end = NULL,
+  data_start = seqs(start > 1),
+  data_end = seqs(end < length),
+  label = "/",
+  size = 4,
+  hjust = 0.75,
+  family = "bold",
+  stat = "identity",
+  na.rm = FALSE,
+  show.legend = NA,
+  inherit.aes = TRUE,
+  ...
+)
+}
+\arguments{
+\item{data_start}{seq_layout of sequences for which to decorate the start.
+default: \code{seqs(start >1)}}
+
+\item{data_end}{seq_layout of sequences for which to decorate the end.
+default: \code{seqs(end < length)}}
+
+\item{label}{the character to decorate ends with. Provide two values for
+different start and end decorations, e.g. \code{label=c("]", "[")}.}
+
+\item{stat}{The statistical transformation to use on the data for this
+layer, either as a \code{ggproto} \code{Geom} subclass or as a string naming the
+stat stripped of the \code{stat_} prefix (e.g. \code{"count"} rather than
+\code{"stat_count"})}
+
+\item{na.rm}{If \code{FALSE}, the default, missing values are removed with
+a warning. If \code{TRUE}, missing values are silently removed.}
+
+\item{show.legend}{logical. Should this layer be included in the legends?
+\code{NA}, the default, includes if any aesthetics are mapped.
+\code{FALSE} never includes, and \code{TRUE} always includes.
+It can also be a named logical vector to finely select the aesthetics to
+display.}
+
+\item{inherit.aes}{If \code{FALSE}, overrides the default aesthetics,
+rather than combining with them. This is most useful for helper functions
+that define both data and aesthetics and shouldn't inherit behaviour from
+the default plot specification, e.g. \code{\link[ggplot2:borders]{borders()}}.}
+
+\item{...}{Other arguments passed on to \code{\link[ggplot2:layer]{layer()}}. These are
+often aesthetics, used to set an aesthetic to a fixed value, like
+\code{colour = "red"} or \code{size = 3}. They may also be parameters
+to the paired geom/stat.}
+}
+\description{
+\code{geom_seq_break()} adds decorations to the ends of truncated sequences. These
+could arise from zooming onto sequence loci with \code{focus()}, or manually
+annotating sequences with start > 1 and/or end < length.
+}
+\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()
+}