tag internals and clean up function reference some more, resolves #25

NAMESPACE

@@ -1,6 +1,5 @@
 # Generated by roxygen2: do not edit by hand
 
-S3method(activate,tbl_genome_layout)
 S3method(add_clusters,gggenomes)
 S3method(add_clusters,gggenomes_layout)
 S3method(add_feats,gggenomes)
@@ -81,8 +80,6 @@ export(PositionPile)
 export(PositionSixframe)
 export(PositionStrand)
 export(PositionStrandpile)
-export(activate)
-export(active)
 export(add_clusters)
 export(add_feats)
 export(add_links)
@@ -190,7 +187,5 @@ importFrom(jsonlite,fromJSON)
 importFrom(magrittr,"%<>%")
 importFrom(magrittr,"%>%")
 importFrom(readr,read_tsv)
-importFrom(rlang,enquo)
-importFrom(rlang,quo_text)
 importFrom(tidyr,unnest)
 importFrom(tidyr,unnest_wider)

R/aaa.R

@@ -24,6 +24,7 @@ swap_if <- function(x, condition, ...){
 #'
 #' @param x vector (coerced to character)
 #' @param collapse character string to separate elements.
+#' @keywords internal
 comma <- function(x, collapse = ","){
     paste(x, collapse=collapse)
 }

R/coords.R

@@ -1,6 +1,7 @@
 #' The virtual x-start of the full length seq in the plot
 #'
 #' Together with the seq strand, this is sufficient to project feats
+#' @keywords internal
 anchor <- function(x, start, strand){
   x - (start-1) * strand_int(strand)
 }
@@ -9,13 +10,14 @@ anchor <- function(x, start, strand){
 #'
 #' @param seq_anchor the virtual x-start of the full length sequence in plot
 #' space
+#' @keywords internal
 x <- function(start, end, strand, seq_x, seq_start, seq_strand){
   a <- anchor(seq_x, seq_start, seq_strand)
   b <- if_reverse(strand, end, start-1)
   a + b * strand_int(seq_strand)
 }
 
-#' @rdname x
+#' @keywords internal
 xend <- function(start, end, strand, seq_x, seq_start, seq_strand){
   a <- anchor(seq_x, seq_start, seq_strand)
   b <- if_reverse(strand, start-1, end)#, end + width(start,end))

R/feats.R

@@ -18,6 +18,7 @@
 #' @param ... passed on to `layout_seqs()`
 #' @return a tbl_df with plot coordinates
 #' @export
+#' @keywords internal
 as_feats <- function(x, seqs, ..., everything=TRUE){
   UseMethod("as_feats")
 }
@@ -66,6 +67,7 @@ as_feats.tbl_df <- function(x, seqs, ..., everything=TRUE){
 #' example after focusing in on a subregion. Choices are to "drop" them, "keep"
 #' them or "trim" them to the subregion boundaries.
 #' @param ... not used
+#' @keywords internal
 layout_feats <- function(x, seqs, keep="strand",
   marginal=c("trim", "drop", "keep"), ...){
   marginal <- match.arg(marginal)

R/gggenomes.R

@@ -90,6 +90,7 @@ gggenomes <- function(seqs=NULL, genes=NULL, feats=NULL, links=NULL, ...,
 #' ggplot.default tries to `fortify(data)` and we don't want that here
 #'
 #' @export
+#' @keywords internal
 ggplot.gggenomes_layout <- function(data, mapping = aes(), ...,
                                environment = parent.frame()) {
   if (!missing(mapping) && !inherits(mapping, "uneval")) {
@@ -134,15 +135,15 @@ layout_genomes <- function(seqs=NULL, genes=NULL, feats=NULL, links=NULL,
       seqs <- mutate(seqs, bin_id = {{ infer_bin_id }})
   }else{
     if(is.null(feats) & is.null(links))
-      stop("Need at least one of: seqs, genes, feats or links")
+      abort("Need at least one of: seqs, genes, feats or links")
 
     # infer dummy seqs
     if(!is.null(feats)){
-      write("No seqs provided, inferring seqs from feats", stderr())
+      inform("No seqs provided, inferring seqs from feats")
       seqs <- infer_seqs_from_feats(feats[[1]], {{infer_bin_id}}, {{infer_start}},
                                      {{infer_end}}, {{infer_length}})
     }else if(!is.null(links)){
-      write("No seqs or feats provided, inferring seqs from links", stderr())
+      inform("No seqs or feats provided, inferring seqs from links")
       seqs <- infer_seqs_from_links(links[[1]],  {{infer_bin_id}}, {{infer_start}},
                                      {{infer_end}}, {{infer_length}})
     }
@@ -165,6 +166,7 @@ layout_genomes <- function(seqs=NULL, genes=NULL, feats=NULL, links=NULL,
 #' and error because dim(gggenome_layout) is undefined. Return dim of primary
 #' table instead
 #' @export
+#' @keywords internal
 dim.gggenomes_layout <- function(x) dim(get_seqs(x))
 
 #' @export

R/links.R

@@ -17,6 +17,7 @@
 #' @param x link data convertible to a link layout
 #' @inheritParams as_feats
 #' @export
+#' @keywords internal
 as_links <- function(x, seqs, ..., everything=TRUE){
     UseMethod("as_links")
 }
@@ -64,6 +65,7 @@ as_links.tbl_df <- function(x, seqs, ..., everything=TRUE){
 #'
 #' @inheritParams as_links
 #' @param ... not used
+#' @keywords internal
 layout_links <- function(x, seqs, keep="strand", adjacent_only = TRUE,
   marginal=c("trim", "drop", "keep"), ...){
   marginal <- match.arg(marginal)

R/pull_tracks.R

@@ -213,6 +213,7 @@ pull_track.gggenomes_layout <- function(.x, .track_id=1, ..., .track_type=NULL,
 #'   giving the position from the left/right.
 #' @param track_type restrict to these types of tracks - affects position-based
 #'   selection
+#' @param ignore_pos names of tracks to ignore when selecting by position.
 #' @return The selected track_id as an unnamed string
 vars_track <- function(x, track_id, track_type = c("seqs", "feats", "links"),
     ignore_pos = NULL){
@@ -246,7 +247,8 @@ vars_track <- function(x, track_id, track_type = c("seqs", "feats", "links"),
     })
 }
 
-#' Error messages for `vars_track``
+#' Error messages for vars_track
+#' @keywords internal
 vars_track_error <- function(bad_value, track_ids, ignore_pos){
   if(is_function(bad_value)) bad_value <- "<function>"
   if(is.numeric(bad_value)) bad_value <- as.character(bad_value)

R/seqs.R

@@ -17,6 +17,7 @@
 #'
 #' as_seqs(chr)
 #' @export
+#' @keywords internal
 as_seqs <- function(x, ...){
     UseMethod("as_seqs")
 }
@@ -164,6 +165,8 @@ get_seqs.gggenomes <- function(x){
 get_seqs.gggenomes_layout <- function(x){
   x$seqs[["seqs"]]
 }
+
+#' @rdname get_seqs
 #' @export
 set_seqs <- function(x, value){
   UseMethod("set_seqs")

R/subfeats.R

@@ -73,6 +73,7 @@ add_subfeat_tracks <- function(x, parent_track_id, tracks, transform){
 #' annotations, e.g. genes and protein blast results.
 #' @return a tbl_df with plot coordinates
 #' @export
+#' @keywords internal
 as_subfeats <- function(x, seqs, feats, ..., everything=TRUE){
   UseMethod("as_subfeats")
 }

R/sublinks.R

@@ -69,6 +69,7 @@ add_sublink_tracks <- function(x, parent_track_id, tracks, transform){
 #' annotations, e.g. genes and protein blast results.
 #' @return a tbl_df with plot coordinates
 #' @export
+#' @keywords internal
 as_sublinks <- function(x, seqs, feats, ..., everything=TRUE){
   UseMethod("as_sublinks")
 }

R/tracks.R

@@ -84,6 +84,7 @@ tracks.gggenomes_layout <- function(x, track_type = c("seqs", "feats", "links"))
 
 
 #' Convert a list of tibbles into tracks with magic
+#' @keywords internal
 as_tracks <- function(tracks, tracks_exprs, reserved_ids=NULL){
   # capture for df naming before first eval of tracks
   track_name <- as_label(enexpr(tracks))

R/vars.R

@@ -29,9 +29,9 @@ require_vars <- function(x, vars, warn_only=FALSE){
 
   if(length(missing_vars) > 0)
     if(warn_only)
-      warning("Required column(s) missing: ", paste(missing_vars, collapse=","))
+      warn(c("Required column(s) missing: ", str_glue("{missing_vars}")))
     else
-      stop("Required column(s) missing: ", paste(missing_vars, collapse=","))
+      abort(c("Required column(s) missing: ", str_glue("{missing_vars}")))
   x
 }
 
@@ -45,6 +45,7 @@ require_vars <- function(x, vars, warn_only=FALSE){
 #' @param any if TRUE not all but at least one variable has to exists
 #' @return TRUE/FALSE
 #' @export
+#' @keywords internal
 has_vars <- function(x, vars, any=FALSE){
   if(any)
     any(vars %in% names(x))
@@ -56,6 +57,7 @@ has_vars <- function(x, vars, any=FALSE){
 #'
 #' equivalent to base::match.arg, but returns all choices on arg=NULL if
 #' several.ok=TRUE
+#' @keywords internal
 match_arg <- function (arg, choices, several.ok = FALSE){
   if (missing(choices)) {
     formal.args <- formals(sys.function(sysP <- sys.parent()))

_pkgdown.yml

@@ -15,10 +15,10 @@ reference:
     - geom_gene
     - geom_feat
     - geom_link
-    - ends_with(c("_text", "_tag", "_note"))
+    - ends_with("_text|_tag|_note")
     - starts_with("geom")
     - starts_with("position_")
-    - starts_with("use_")
+    - starts_with("theme_")
 - title: "Manipulate plot & data"
 - contents:
     - pick
@@ -37,37 +37,21 @@ reference:
     - file_formats
     - def_names
     - def_types
+    - starts_with("write")
 - title: "Under the hood"
   desc: >
     Functions that power gggenomes under the hood. Useful for developers and power-users.
 - contents:
   - layout
-  - layout_feats
-  - layout_links
-  - require_vars
   - get_seqs
-  - starts_with("as_")
+  - starts_with("track")
+  - require_vars
+  - vars_track
   - swap_if
   - in_range
-  - anchor
   - width
-  - x
-  - track_ids
-  - track_types
-  - vars_track
-  - activate
-  - comma
-  - dim.gggenomes_layout
-  - ggplot.gggenomes_layout
-  - has_vars
   - introduce
-  - match_arg
-  - theme_gggenomes_clean
-  - track_nrows
-  - track_type
-  - vars_track_error
-  - write_gff3
-- title: "Handling files"
+- title: "Handle files"
 - contents:
   - ext_to_format
   - file_exts
@@ -78,8 +62,6 @@ reference:
 figures:
   fig.width: 10
   fig.height: 5
-  #  dev.args:
-  #  type: "cairo"
 template:
   params:
     bootswatch: cosmo