updated shift() example, fixes #163

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