## ----initial-clearPlot, eval=TRUE, echo=FALSE, fig.keep='none', message=FALSE----
quickPlot::clearPlot()

## ----load_files, eval=TRUE, echo=TRUE, message=FALSE, fig.height=2------------
#  Make list of maps from package database to load, and what functions to use to load them
library(data.table)
library(terra)
library(quickPlot)

# omit forestAge and percentPine maps for simplicity
files <- system.file("maps", package = "quickPlot") |>
  dir(full.names = TRUE, pattern = "tif")
filelist <- data.frame(file = files[-c(2, 5)], stringsAsFactors = FALSE)
print(filelist)

# Load files to memory (using rasterToMemory), assign to a simList we call maps
maps <- lapply(filelist$file, function(x) rast(x))
names(maps) <- sapply(basename(filelist$file), function(x) {
  strsplit(x, split = "\\.")[[1]][1]
})

# put into a single stack object in the simulation environment for ease of use below
landscape <- c(maps$DEM, maps$forestCover, maps$habitatQuality)

## ----first_plot, eval=TRUE, echo=TRUE, fig.height=2---------------------------
Plot(landscape, new = TRUE)
# make a SpatialPoints object
caribou <- terra::vect(cbind(
  x = stats::runif(1e2, -50, 50),
  y = stats::runif(1e2, -50, 50)
))
Plot(caribou)
Plot(caribou, addTo = "landscape$habitatQuality")

# from ?vect help file
x1 <- rbind(c(-18, -2), c(-14, 5.5), c(1, 0), c(-14, -6))
x2 <- rbind(c(-1, 0), c(14, 6), c(16, 0), c(14, -5.5))
x3 <- rbind(c(-12.5, 0), c(0, 6), c(4, 0.5), c(1.5, -4.5))
hole <- rbind(c(8, 0), c(10.5, 1.3), c(12, 0.2), c(10.5, -1.3))
z <- rbind(
  cbind(object = 1, part = 1, x1, hole = 0),
  cbind(object = 2, part = 1, x3, hole = 0),
  cbind(object = 3, part = 1, x2, hole = 0),
  cbind(object = 3, part = 1, hole, hole = 1)
)
colnames(z)[3:4] <- c("x", "y")
spP <- terra::vect(z, "polygons")

Plot(spP)
Plot(spP, addTo = "landscape$habitatQuality", gp = gpar(lwd = 2))

## from ?vect help file
z[z[, "hole"] == 1, "object"] <- 4
sl <- vect(z[, 1:4], "lines")

Plot(sl, gp = gpar(col = c("red", "blue"), lwd = 2), addTo = "landscape$DEM")

## ----mixing_layer_types, eval=TRUE, echo=TRUE, fig.height=5-------------------
clearPlot()
Plot(landscape, caribou, maps$DEM, spP,
  axes = TRUE,
  gp = gpar(cex = 0.5), visualSqueeze = 0.65
)

## ----ggplot, eval=TRUE, echo=TRUE, cache=FALSE, fig.height=2------------------
if (requireNamespace("ggplot2")) {
  ggObj <- data.frame(x = stats::rnorm(1e3)) |>
    ggplot2::ggplot(ggplot2::aes(x = x)) +
    ggplot2::geom_histogram()
  clearPlot()
  Plot(caribou, axes = "L", new = TRUE)
  Plot(ggObj)
}

## ----base-objects, eval=FALSE, echo=TRUE, cache=FALSE, fig.height=2-----------
# baseObj <- rnorm(1e3)
# baseObj2 <- baseObj * 1.2 + rnorm(1e3)
# clearPlot()
# # Plot(baseObj, axes = "L", ylab = "Something meaningful")
# Plot(baseObj, baseObj2, addTo = "scatterplot", axes = TRUE)
# newPoints <- rnorm(10)
# newPoints2 <- newPoints * 1.2 + rnorm(10)
# Plot(newPoints, newPoints2, addTo = "scatterplot", col = "red")

## ----set_colours, eval=TRUE, echo=TRUE, fig.height=2--------------------------
# can change colour palette
clearPlot()
Plot(landscape) # original

# can use RColorBrewer if installed
habQualCols <- if (requireNamespace("RColorBrewer")) {
  RColorBrewer::brewer.pal(9, "Spectral")
} else {
  colorRampPalette(c("blue", "purple"))(9)
}

mapColours <- list(
  DEM = topo.colors(50),
  forestCover = colorRampPalette(c("blue", "orange", "purple", "red"))(50),
  habitatQuality = habQualCols
)
setColors(landscape, n = 50) <- mapColours
Plot(landscape, new = TRUE) # oh, how pretty!

## ----gp_gpAxis_gpText, eval=TRUE, echo=TRUE, fig.height=2---------------------
clearPlot()
Plot(caribou, gpAxis = gpar(cex = 0.4), size = 1)
Plot(maps$DEM, gpText = gpar(cex = 0.4))
clearPlot()
Plot(maps$DEM, caribou, gpText = list(gpar(cex = 2), gpar(cex = 0.1)), new = TRUE)

## ----visualSqueeze, eval=TRUE, echo=TRUE, fig.height=2------------------------
# x axis gets cut off in pdf and html
clearPlot()
Plot(maps$DEM)
clearPlot()
Plot(maps$DEM, visualSqueeze = 0.6, new = TRUE)

## ----legendRange, eval=TRUE, echo=TRUE, fig.height=2--------------------------
clearPlot()
Plot(maps$DEM, legendRange = c(0, 500), new = TRUE)

## ----zoomExtent, eval=TRUE, echo=TRUE, fig.height=2---------------------------
Plot(maps$DEM, zoomExtent = terra::ext(c(-1, 10, -1, 20)), new = TRUE)

## ----arrows, eval=TRUE, echo=TRUE, fig.height=2-------------------------------
clearPlot()
Plot(maps$DEM)
Plot(sl, addTo = "maps$DEM", length = 0.2)

## ----new-as-list--------------------------------------------------------------
clearPlot()
Plot(landscape)
Plot(landscape, new = list(TRUE, FALSE, TRUE), axes = "L")

## ----simple_add, eval=TRUE, echo=TRUE, fig.height=3---------------------------
clearPlot()
Plot(landscape)
# can add a new plot to the plotting window
Plot(caribou, new = FALSE, axes = FALSE)

## ----add_with_rearrangement, eval=TRUE, echo=TRUE, fig.height=2---------------
clearPlot()
Plot(landscape)
# can add a new plot to the plotting window
Plot(caribou, new = FALSE, axes = FALSE)

## ----add_with_same_name, eval=TRUE, echo=TRUE, fig.height=2-------------------
clearPlot()
Plot(landscape)
landscape$forestCover[] <- ((landscape$forestCover[] + 10) %% 30)
# can add a new plot to the plotting window
Plot(landscape, new = FALSE)
# note: zeros are treated as no colour by default.
# if this is not the correct behaviour, can use `zero.color`
Plot(landscape, new = FALSE, zero.color = "blue")

## ----speedup, eval=TRUE, echo=TRUE, fig.height=2------------------------------
system.time(Plot(landscape, caribou, maps$DEM, new = TRUE))
system.time(Plot(landscape, caribou, maps$DEM, speedup = 10, new = TRUE))
# can add a new plot to the plotting window

## ----add, eval=TRUE, echo=TRUE, fig.height=2----------------------------------
clearPlot()
Plot(landscape)
Plot(caribou, addTo = "landscape$DEM", size = 2)

## ----clearPlot, eval=TRUE, echo=TRUE, fig.height=2----------------------------
clearPlot()
Plot(caribou)

## ----clickValues, eval=FALSE, echo=TRUE---------------------------------------
# clearPlot()
# Plot(landscape)
# clickValues(3) # click at three locations on the Plot device

## ----clickExtent, eval=FALSE, echo=TRUE---------------------------------------
# clearPlot()
# Plot(landscape)
# clickExtent() # click at two locations on the Plot device

## ----rePlot, eval=FALSE, echo=TRUE, cache=FALSE-------------------------------
# rePlot()
# rePlot(4)
# rePlot(visualSqueeze = 1, axes = FALSE)
# rePlot(visualSqueeze = 0.7, axes = FALSE, cols = "Reds")

## ----Plot a .quickPlot object, eval=FALSE, echo=TRUE, cache=FALSE-------------
# clearPlot()
# plots <- Plot(landscape)
# 
# # change values
# landscape$forestCover[landscape$habitatQuality > 0.9] <- 0
# 
# Plot(plots)
# # same as:
# rePlot()
# 
# # but can be combined with other objects
# Plot(caribou, plots)
# Plot(caribou, plots, sl)