ggGS: Prepare data in 'MPG' and 'grain' objects for use with...

In achubaty/grainscape: Landscape Connectivity, Habitat, and Protected Area Networks

Prepare data in MPG and grain objects for use with ggplot2

Description

This is an informal fortify-type method that prepares either RasterLayer or igraph objects contained as slots within MPG or grain objects for easy plotting with ggplot().

Usage

ggGS(x, type = NULL, ...)

## S4 method for signature 'RasterLayer'
ggGS(x, type = NULL, ...)

## S4 method for signature 'list'
ggGS(x, type = NULL, ...)

## S4 method for signature 'mpg'
ggGS(x, type = NULL, ...)

## S4 method for signature 'grain'
ggGS(x, type = NULL, ...)

## S4 method for signature 'goc'
ggGS(x, type = NULL, ...)

Arguments

x	A mpg, grain, or RasterLayer object.
type	If a mpg or grain object is supplied, this gives the name of the slot to prepare for plotting. Options are discussed below. Not required if a RasterLayer is supplied.
...	Additional arguments (not used).

Value

A data.frame suitable for plotting with ggplot().

Where type is a raster the data.frame will have the following columns:

value

the value of the raster cell

x

the x coordinate of the centre of the raster cell

y

the y coordinate of the centre of the raster cell

Where type = 'nodes' the data.frame will have the following columns:

x

the x coordinate of the node

y

the y coordinate of the node

...

other attributes associated with the network nodes

Where type = 'links' the data.frame will have the following columns:

x1

the x coordinate of the first node

y1

the y coordinate of the first node

x2

the x coordinate of the second node

y2

the y coordinate of the second node

x1p

the x coordinate at the perimeter of the first node

y1p

the y coordinate at the perimeter of the first node

x2p

the x coordinate at the perimeter of the second node

y2p

the y coordinate at the perimeter of the second node

...

other attributes associated with the network links

Note

Options for type parameter

If a RasterLayer is supplied type is optional.

For mpg type options are "node" or "links". This prepares the nodes and links of the minimum planar graph network for plotting, Also "patchId", "voronoi", "lcpPerimWeight", "lcpLinkId", "mpgPlot" will prepare rasters for plotting.

For grain objects type options are "nodes" or"links" to prepare the nodes and links of the grains of connectivity network for plotting. Also "voronoi" will prepare the grains of connectivity Voronoi polygons raster for plotting.

For either mpg or grain objects type = "vorBound" will identify the boundaries of the Voronoi polygons for plotting. This is potentially time consuming for large rasters.

Author(s)

Paul Galpern and Alex Chubaty

See Also

MPG(), GOC()

Examples

## Load raster landscape
tiny <- raster::raster(system.file("extdata/tiny.asc", package = "grainscape"))

## Create a resistance surface from a raster using an is-becomes reclassification
tinyCost <- raster::reclassify(tiny, rcl = cbind(c(1, 2, 3, 4), c(1, 5, 10, 12)))
## Produce a patch-based MPG where patches are resistance features=1
tinyPatchMPG <- MPG(cost = tinyCost, patch = tinyCost == 1)
## Extract a representative subset of 5 grains of connectivity
tinyPatchGOC <- GOC(tinyPatchMPG, nThresh = 5)
if (interactive()) {
  library(ggplot2)

  ## Plot the patches in a minimum planar graph
  theme_set(theme_grainscape())
  ggplot() +
    geom_tile(data = ggGS(tinyPatchMPG, "patchId"),
              aes(x = x, y = y, fill = value))

  ## Plot the grain polygons in a grain of connectivity
  ggplot() +
    geom_tile(data = ggGS(grain(tinyPatchGOC, 3), "voronoi"),
              aes(x = x, y = y, fill = value))

  ## Plot the grain polygon boundaries
  ggplot() +
    geom_tile(data = ggGS(grain(tinyPatchGOC, 3), "vorBound"),
              aes(x = x, y = y, fill = value))

  ## Plot the patches and perimeter links of a minimum planar graph
  ggplot() +
    geom_tile(data = ggGS(tinyPatchMPG, "patchId"),
              aes(x = x, y = y, fill = value)) +
    geom_segment(data = ggGS(tinyPatchMPG, "links"),
                 aes(x = x1p, y = y1p, xend = x2p, yend = y2p))

  ## Plot the patches and linear representations of the perimeter links
  ## of a minimum planar graph
  ggplot() +
    geom_tile(data = ggGS(tinyPatchMPG, "patchId"),
              aes(x = x, y = y, fill = value)) +
    geom_segment(data = ggGS(tinyPatchMPG, "links"),
                 aes(x = x1p, y = y1p, xend = x2p, yend = y2p))

  ## Plot the nodes and links of a grains of connectivity network
  ## superimposed over the grain polygons
  focalGrain <- grain(tinyPatchGOC, 3)
  ggplot() +
    geom_tile(data = ggGS(focalGrain, "vorBound"),
              aes(x = x, y = y, fill = value)) +
    geom_point(data = ggGS(focalGrain, "nodes"),
               aes(x = x, y = y)) +
    geom_segment(data = ggGS(focalGrain, "links"),
                 aes(x = x1, y = y1, xend = x2, yend = y2))
}

achubaty/grainscape documentation built on Jan. 4, 2025, 8:43 a.m.