From 2f7423093df8d740b7899fa8b9181e59a8e4d9d9 Mon Sep 17 00:00:00 2001
From: Thomas Hackl <thackl@lim4.de>
Date: Sun, 15 Oct 2023 21:14:31 +0200
Subject: [PATCH] updated shift() example, fixes #163

---
 R/shift.R    | 33 +++++++++++++++++----------------
 man/shift.Rd | 29 +++++++++++++++--------------
 2 files changed, 32 insertions(+), 30 deletions(-)

diff --git a/R/shift.R b/R/shift.R
index 4f43a62..24dd3e7 100644
--- a/R/shift.R
+++ b/R/shift.R
@@ -7,22 +7,23 @@
 #' @param by shift each bin by this many bases. Single value or vector of the
 #' same length as bins.
 #' @examples
-#' # Basic example plot
-#' gggenomes(seqs = emale_seqs) |>
-#' geom_seq() +
-#' geom_bin_label() 
-#' 
-#' # All bins have been shifted 10000 basepaiers
-#' gggenomes(seqs = emale_seqs) |>
-#' shift(bins = everything(), by = 10000)
-#' geom_seq() +
-#' geom_bin_label() 
-#' 
-#' # Only RCC970_016B bin has been shifted for 5000 basepaiers
-#' gggenomes(seqs = emale_seqs) |>
-#' shift(bins = RCC970_016B, by = 5000, center = FALSE)
-#' geom_seq() +
-#' geom_bin_label() 
+#' p0 <- gggenomes(emale_genes, emale_seqs) +
+#' geom_seq() + geom_gene()
+#'
+#' # Slide one bin left and one bin right
+#' p1 <- p0 |> shift(2:3, by=c(-8000, 10000))
+#'
+#' # align all bins to a target gene
+#' mcp <- emale_genes |>
+#'   filter(name == "MCP") |>
+#'   group_by(seq_id) |>
+#'   slice_head(n=1) # some have fragmented MCP gene, keep only first
+#'
+#' p2 <- p0 |> shift(all_of(mcp$seq_id), by= -mcp$start) +
+#'   geom_gene(data=genes(name=="MCP"), fill="#01b9af")
+#'
+#' library(patchwork)
+#' p0 + p1 + p2
 #' @export
 shift <- function(x, bins=everything(), by=0, center=FALSE){
   # split by bin_id and select bins
diff --git a/man/shift.Rd b/man/shift.Rd
index dbed65c..f018e51 100644
--- a/man/shift.Rd
+++ b/man/shift.Rd
@@ -17,20 +17,21 @@ Shift bins along the x-axis, i.e. left or right in the default plot
 layout. This is useful to align feats of interest in different bins.
 }
 \examples{
-# Basic example plot
-gggenomes(seqs = emale_seqs) |>
-geom_seq() +
-geom_bin_label() 
+p0 <- gggenomes(emale_genes, emale_seqs) +
+geom_seq() + geom_gene()
 
-# All bins have been shifted 10000 basepaiers
-gggenomes(seqs = emale_seqs) |>
-shift(bins = everything(), by = 10000)
-geom_seq() +
-geom_bin_label() 
+# Slide one bin left and one bin right
+p1 <- p0 |> shift(2:3, by=c(-8000, 10000))
 
-# Only RCC970_016B bin has been shifted for 5000 basepaiers
-gggenomes(seqs = emale_seqs) |>
-shift(bins = RCC970_016B, by = 5000, center = FALSE)
-geom_seq() +
-geom_bin_label() 
+# align all bins to a target gene
+mcp <- emale_genes |>
+  filter(name == "MCP") |>
+  group_by(seq_id) |>
+  slice_head(n=1) # some have fragmented MCP gene, keep only first
+
+p2 <- p0 |> shift(all_of(mcp$seq_id), by= -mcp$start) +
+  geom_gene(data=genes(name=="MCP"), fill="#01b9af")
+
+library(patchwork)
+p0 + p1 + p2
 }