more example namespace fixes

thackl · Oct 16, 2023 · 6b93c05 · 6b93c05
1 parent 95d5a5c
commit 6b93c05
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Showing 3 changed files with 3 additions and 3 deletions.
diff --git a/R/focus.R b/R/focus.R
@@ -63,7 +63,7 @@
 #' f1 <- f0 %>%
 #'   # parser system/gene info
 #'   tidyr::separate(seq_id2, into=c("seq_id2", "system", "gene"), sep=",") %>%
-#'   filter(
+#'   dplyr::filter(
 #'     evalue < 1e-10,  # get rid of some spurious hits
 #'     # and let's focus just on a few systems for this example
 #'     system %in% c("CRISPR-CAS", "DISARM", "GABIJA", "LAMASSU", "THOERIS"))

diff --git a/R/geom.R b/R/geom.R
@@ -151,7 +151,7 @@ geom_seq_label <- function(mapping = NULL, data = seqs(),
 #' @export
 #' @examples
 #' s0 <- read_seqs(list.files(ex("cafeteria"), "Cr.*\\.fa", full.names = TRUE))
-#' s1 <- s0 %>% filter(length>5e5)
+#' s1 <- s0 %>% dplyr::filter(length>5e5)
 #'
 #' gggenomes(emale_genes) + geom_seq() + geom_gene() +
 #'   geom_bin_label()

diff --git a/R/shift.R b/R/shift.R
@@ -17,7 +17,7 @@
 #' mcp <- emale_genes |>
 #'   filter(name == "MCP") |>
 #'   group_by(seq_id) |>
-#'   slice_head(n=1) # some have fragmented MCP gene, keep only first
+#'   dplyr::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")