Handle features of origin of plasmid

.github/workflows/R-CMD-check.yaml

@@ -31,6 +31,7 @@ jobs:
           - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
           - {os: ubuntu-latest,   r: 'release'}
           - {os: ubuntu-latest,   r: 'oldrel-1'}
+          - {os: ubuntu-latest,   r: 'oldrel-2'}
 
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/pkgdown.yaml

@@ -19,6 +19,8 @@ jobs:
       group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
     steps:
       - uses: actions/checkout@v3
 

.gitignore

@@ -1,4 +1,5 @@
-.Rproj.user
-.Rhistory
-.RData
-.Ruserdata
+.Rproj.user
+.Rhistory
+.RData
+.Ruserdata
+docs

DESCRIPTION

@@ -33,6 +33,7 @@ Suggests:
     testthat (>= 3.0.0)
 VignetteBuilder: knitr
 Depends: R (>= 2.10)
-URL: https::/github.com/bradyajohnston/plasmapr
-BugReports: https://github.com/bradyajohnston/plasmapr/issues
+URL: https://github.com/BradyAJohnston/plasmapr, https://bradyajohnston.github.io/plasmapR/
+BugReports: https://github.com/BradyAJohnston/plasmapR/issues
 Config/testthat/edition: 3
+Config/testthat/parallel: true

NAMESPACE

@@ -5,4 +5,5 @@ export(StatArrow)
 export(StatArrowLabel)
 export(plot_plasmid)
 export(read_gb)
+export(stat_arrow)
 importFrom(rlang,.data)

R/dataframe.R

@@ -1,12 +1,4 @@
-.feature_list_to_df <- function(x) {
-  # dat <- data.frame(
-  #   index = numeric(),
-  #   name = character(),
-  #   type = character(),
-  #   start = numeric(),
-  #   end = numeric(),
-  #   direction = numeric()
-  # )
+.feature_list_to_df <- function(x, bp = NULL, ...) {
 
   feats <- lapply(seq(length(x)), \(i) {
     feat <- x[[i]]
@@ -22,13 +14,27 @@
   })
 
   dat <- do.call(rbind, feats)
-  # }
 
   # turn certain features in to numeric columns
   dat$start <- as.numeric(dat$start)
   dat$end <- as.numeric(dat$end)
   dat$direction <- as.numeric(dat$direction)
 
+  over_origin <- dat$start > dat$end & dat$direction == 1
+
+  if (any(over_origin)) {
+    offset <- dat$end[over_origin] + 1
+
+    if (is.null(bp)) {
+      bp <- max(c(dat$start, dat$end))
+    }
+
+    dat$start <- dat$start - offset
+    dat$end <- dat$end - offset
+
+    dat$end[over_origin] <- bp
+
+  }
 
 # only return features where a start was successfully parsed
   # dat[!is.na(dat$start), ]
@@ -46,5 +52,5 @@
 #' @rdname as.data.frame.plasmid
 #' @export
 as.data.frame.plasmid <- function(x, row.names, optional, ...) {
-  .feature_list_to_df(x$features)
+  .feature_list_to_df(x$features, bp = x$length)
 }

R/get.R

@@ -13,15 +13,14 @@
 }
 
 .get_start_end <- function(x) {
-  vector <- stringr::str_extract(x, "\\d+\\.\\.\\d+") |>
-    stringr::str_split("\\.\\.") |>
-    unlist() |>
-    as.numeric()
-  if (length(vector) == 1) {
-    c(vector, vector)
-  } else {
-    vector
-  }
+  start_stops <- stringr::str_extract_all(x, "\\d+\\.\\.\\d+")[[1]]
+  numbers <- unlist(stringr::str_extract_all(start_stops, "\\d+"))
+  numbers <- as.numeric(numbers)
+
+  # takes into account where there is a join(500..600, 1..100)
+  # where the feature goes over the origin
+  vector <- c(numbers[1], numbers[length(numbers)])
+  vector
 }
 
 .get_feature_type <- function(x) {

R/plot.R

@@ -1,7 +1,13 @@
 
 #' @importFrom rlang .data
 #' @noRd
-.plot_plasmid <- function(dat, bp, name = "Plasmid Name", label_wrap = 20) {
+.plot_plasmid <- function(
+    dat,
+    bp,
+    name = "Plasmid Name",
+    rotation = 0,
+    label_wrap = 20
+    ) {
   dat <- dat[dat$type != "source", ]
 
   name_supplied <- !is.null(name) & name != ""
@@ -22,7 +28,7 @@
     )) +
     ggplot2::geom_hline(yintercept = yintercept) +
     ggplot2::coord_polar(
-      start = pi / 4
+      start = rotation
       ) +
 
 
@@ -91,7 +97,7 @@
 #' @export
 plot_plasmid <- function(plasmid, name = "Plasmid Name", label_wrap = 20) {
   if (methods::is(plasmid, "plasmid")) {
-    features <- as.data.frame(plasmid)
+    features <- as.data.frame(plasmid, bp = plasmid$length)
   } else if (methods::is(plasmid, "data.frame")) {
     features <- plasmid
   } else {

R/stat_arrow.R

@@ -154,34 +154,58 @@ StatArrowLabel <- ggplot2::ggproto('StatArrowLabel', StatArrow,
   # required_aes = c('start', 'end')
 )
 
-stat_arrow <-
-  function(mapping = NULL,
-           data = NULL,
-           geom = "polygon",
-           position = "identity",
-           na.rm = FALSE,
-           show.legend = NA,
-           inherit.aes = TRUE,
-           ...,
-           bp = 6000,
-           # middle = 4,
-           arrowhead_size = 8
-           ) {
-    ggplot2::layer(
-      stat = "arrow",
-      data = data,
-      mapping = mapping,
-      geom = geom,
-      position = position,
-      show.legend = show.legend,
-      inherit.aes = inherit.aes,
-      params = list(
-        na.rm = na.rm,
-        bp = bp,
-        # middle = middle,
-        arrowhead_size = arrowhead_size,
-        # start = start,
-        # end = end,
-        ...)
+#' Custom Stat: Arrow
+#'
+#' This stat creates arrow shapes in a ggplot.
+#'
+#' @param mapping The aesthetic mapping, usually constructed with aes().
+#' @param data The dataset to be used in the layer.
+#' @param geom The geometric object to use for the layer, default is "polygon".
+#' @param position Position adjustment, default is "identity".
+#' @param na.rm Should missing values be removed?
+#' @param show.legend Logical. Should this layer be included in the legends?
+#' @param inherit.aes Should inherit aesthetics from the parent plot?
+#' @param ... Other arguments passed to layer().
+#' @param bp The base parameter for the arrow shape.
+#' @param arrowhead_size The size of the arrowhead.
+#' @return A ggplot layer with arrow shapes.
+#' @export
+#'
+#' @seealso \code{\link[ggplot2]{geom_segment}}
+#'
+#' @details
+#' Used for drawing features for a plasmid that work in both cartesian and
+#' polad coordinate systems.
+#'
+#' @note
+#' The `bp` parameter determines the base parameter of the arrow shape.
+#' The `arrowhead_size` parameter controls the size of the arrowhead.
+#'
+#' @keywords plotting
+stat_arrow <- function(mapping = NULL,
+                       data = NULL,
+                       geom = "polygon",
+                       position = "identity",
+                       na.rm = FALSE,
+                       show.legend = NA,
+                       inherit.aes = TRUE,
+                       ...,
+                       bp = 6000,
+                       arrowhead_size = 8
+) {
+  ggplot2::layer(
+    stat = "arrow",
+    data = data,
+    mapping = mapping,
+    geom = geom,
+    position = position,
+    show.legend = show.legend,
+    inherit.aes = inherit.aes,
+    params = list(
+      na.rm = na.rm,
+      bp = bp,
+      arrowhead_size = arrowhead_size,
+      ...
     )
-  }
+  )
+}

_pkgdown.yml

@@ -1,12 +1,12 @@
-url: https://bradyajohnston.github.io/plasmapr
-
-authors:
-  Brady Johnston:
-    href: https://bradyajohnston.github.io
-
-template:
-  params:
-    bootswatch: flatly
-    ganalytics: G-Z2J58R6DJC
-    docsearch:
-      index_name: plasmapr
+url: https://github.com/bradyajohnston/plasmapR, https://bradyajohnston.github.io/plasmapR/
+
+authors:
+  Brady Johnston:
+    href: https://bradyajohnston.github.io
+
+template:
+  params:
+    bootswatch: flatly
+    ganalytics: G-Z2J58R6DJC
+    docsearch:
+      index_name plasmapr