## ----setup, include = FALSE---------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.width = 6,
  fig.height = 6,
  dpi = 110
)
library(plasmidplot)

## ----scratch------------------------------------------------------------------
p <- plasmid("pBR322", 4361) |>
  pp_marker(86, 1276,   label = "TcR",  arrow = "end") |>
  pp_marker(1915, 2106, label = "rop",  arrow = "start") |>
  pp_marker(2535, 3122, label = "ori") |>
  pp_marker(3293, 4153, label = "AmpR", arrow = "start")

plot(p)

## ----wrap---------------------------------------------------------------------
plot(pp_marker(plasmid("pWrap", 3000), 2800, 300, label = "crosses origin",
               arrow = "end"))

## ----features-----------------------------------------------------------------
feats <- data.frame(
  start = c(86, 2535, 3293),
  end   = c(1276, 3122, 4153),
  label = c("TcR", "ori", "AmpR"),
  arrow = c("end", "none", "start")
)
plot(pp_features(plasmid("pBR322", 4361), feats))

## ----read---------------------------------------------------------------------
gb <- system.file("extdata", "pDemo.gb", package = "plasmidplot")
p <- read_plasmid(gb)
p

## ----read-args, eval = FALSE--------------------------------------------------
# read_genbank(gb,
#   types      = "CDS",        # keep only these feature types
#   skip_types = "source",     # drop these (source spans the whole molecule)
#   label_from = c("label", "gene", "product"),  # qualifier priority
#   color_by   = "feature",    # or "type": one color per feature type
#   colors     = "style",      # or "file": keep the colors stored in the file
#   sequence   = TRUE          # keep the sequence for pp_find_sites()
# )

## ----sites, fig.height = 6.5--------------------------------------------------
p <- pp_find_sites(p)
plot(p)

## ----sites-args, eval = FALSE-------------------------------------------------
# pp_find_sites(p, c("EcoRI", "BamHI"))
# pp_find_sites(p, c(MyEnz = "GGWCC"))
# pp_find_sites(p, unique_only = FALSE, max_sites = 3)

## ----style-scratch------------------------------------------------------------
plot(p, style = pp_style(anchor = "outside", backbone = "line",
                         radius = 0.26, arc = 0.05))

## ----style-preset-------------------------------------------------------------
plot(p, style = pp_style("minimal", arc = 0.05))

## ----presets------------------------------------------------------------------
pp_style()

## ----canvas-------------------------------------------------------------------
plot(p, style = "neon", bg = pp_canvas("neon"))

## ----linear, fig.width = 8, fig.height = 4------------------------------------
plot(p, style = pp_style("angular", layout = "linear"))

## ----palettes-----------------------------------------------------------------
pp_palette()
plot(p, style = pp_style("angular", palette = "jewel"))

## ----external, eval = FALSE---------------------------------------------------
# plot(p, style = pp_style("angular", palette = ggsci::pal_npg("nrc")))
# plot(p, style = pp_style("angular", palette = RColorBrewer::brewer.pal(8, "Dark2")))

## ----check--------------------------------------------------------------------
pp_check_palette("default")

## ----panels, fig.width = 8, fig.height = 4------------------------------------
grid::grid.newpage()
grid::pushViewport(grid::viewport(layout = grid::grid.layout(1, 2)))
grid::pushViewport(grid::viewport(layout.pos.col = 1))
plot(p, style = pp_style("angular", show_title = FALSE), newpage = FALSE)
grid::popViewport()
grid::pushViewport(grid::viewport(layout.pos.col = 2))
plot(p, style = pp_style("minimal", show_title = FALSE), newpage = FALSE)
grid::popViewport(2)

## ----unicode, eval = FALSE----------------------------------------------------
# ragg::agg_png("plasmid.png", width = 1400, height = 1400, res = 220)
# plot(p)
# dev.off()