Plot

0th

Percentile

Plot: Fast, optimally arranged, multipanel plotting function with SpaDES

The main plotting function accompanying SpaDES. This can take objects of type Raster*, SpatialPoints*, SpatialPolygons*, and any combination of those. It can also handle ggplot2 objects or base::histogram objects via call to exHist <- hist(1:10, plot = FALSE). Customization of the ggplot2 elements can be done as a normal ggplot2 plot, then added with Plot(ggplotObject).

Re-plot to a specific device

Usage
Plot(..., new = FALSE, addTo = NULL, gp = gpar(), gpText = gpar(), gpAxis = gpar(), axes = FALSE, speedup = 1, size = 5, cols = NULL, zoomExtent = NULL, visualSqueeze = NULL, legend = TRUE, legendRange = NULL, legendText = NULL, pch = 19, title = TRUE, na.color = "#FFFFFF00", zero.color = NULL, length = NULL)
"Plot"(..., new = FALSE, addTo = NULL, gp = gpar(), gpText = gpar(), gpAxis = gpar(), axes = FALSE, speedup = 1, size = 5, cols = NULL, zoomExtent = NULL, visualSqueeze = NULL, legend = TRUE, legendRange = NULL, legendText = NULL, pch = 19, title = TRUE, na.color = "#FFFFFF00", zero.color = NULL, length = NULL)
"Plot"(..., new = FALSE, addTo = NULL, gp = gpar(), gpText = gpar(), gpAxis = gpar(), axes = FALSE, speedup = 1, size = 5, cols = NULL, zoomExtent = NULL, visualSqueeze = NULL, legend = TRUE, legendRange = NULL, legendText = NULL, pch = 19, title = TRUE, na.color = "#FFFFFF00", zero.color = NULL, length = NULL)
rePlot(toDev = dev.cur(), fromDev = dev.cur(), ...)
Arguments
...
A combination of spatialObjects or some non-spatial objects. See details.
new
Logical. If TRUE, then the previous plot is wiped and a new one made; if FALSE, then the ... plots will be added to the current device, adding or rearranging the plot layout as necessary. Default is FALSE.
addTo
Character vector, with same length as .... This is for overplotting, when the overplot is not to occur on the plot with the same name, such as plotting a SpatialPoints* object on a RasterLayer.
gp
A gpar object, created by gpar function, to change plotting parameters (see grid package).
gpText
A gpar object for the title text. Default gpar(col = "black").
gpAxis
A gpar object for the axes. Default gpar(col = "black").
axes
Logical or "L", representing the left and bottom axes, over all plots.
speedup
Numeric. The factor by which the number of pixels is divided by to plot rasters. See Details.
size
Numeric. The size, in points, for SpatialPoints symbols, if using a scalable symbol.
cols
(also col) Character vector or list of character vectors of colours. See details.
zoomExtent
An Extent object. Supplying a single extent that is smaller than the rasters will call a crop statement before plotting. Defaults to NULL. This occurs after any downsampling of rasters, so it may produce very pixelated maps.
visualSqueeze
Numeric. The proportion of the white space to be used for plots. Default is 0.75.
legend
Logical idicating whether a legend should be drawn. Default is TRUE.
legendRange
Numeric vector giving values that, representing the lower and upper bounds of a legend (i.e., 1:10 or c(1,10) will give same result) that will override the data bounds contained within the grobToPlot.
legendText
Character vector of legend value labels. Defaults to NULL, which results in a pretty numeric representation. If Raster* has a Raster Attribute Table (rat; see raster package), this will be used by default. Currently, only a single vector is accepted. The length of this must match the length of the legend, so this is mosty useful for discrete-valued rasters.
pch
see ?par.
title
Logical indicating whether the names of each plot should be written above plots.
na.color
Character string indicating the color for NA values. Default transparent.
zero.color
Character string indicating the color for zero values, when zero is the minimum value, otherwise, zero is treated as any other color. Default transparent.
length
Numeric. Optional length, in inches, of the arrow head.
toDev
Numeric. Which device should the new rePlot be plotted to. Default is current device.
fromDev
Numeric. Which device should the replot information be taken from. Default is current device
Details

NOTE: Plot uses the grid package; therefore, it is NOT compatible with base R graphics. Also, because it does not by default wipe the plotting device before plotting, a call to clearPlot could be helpful to resolve many errors.

If new = TRUE, a new plot will be generated. This is equivalent to calling clearPlot(); Plot(Object), i.e,. directly before creating a new Plot. When new = FALSE, any plot that already exists will be overplotted, while plots that have not already been plotted will be added. This function rearranges the plotting device to maximize the size of all the plots, minimizing white space. If using the RStudio IDE, it is recommended to make and use a new device with dev(), because the built in device is not made for rapid redrawing. The function is based on the grid package.

Each panel in the multipanel plot must have a name. This name is used to overplot, rearrange the plots, or overlay using addTo when necessary. If the ... are named spatialObjects, then Plot will use these names. However, this name will not persist when there is a future call to Plot that forces a rearrangement of the plots. A more stable way is to use the object names directly, and any layer names (in the case of RasterLayer or RasterStack objects). If plotting a RasterLayer and the layer name is "layer" or the same as the object name, then, for simplicity, only the object name will be used. In other words, only enough information is used to uniquely identify the plot.

cols is a vector of colours that can be understood directly, or by colorRampePalette, such as c("orange", "blue"), will give a colour range from orange to blue, interploated. If a list, it will be used, in order, for each item to be plotted. It will be recycled if it is shorter than the objects to be plotted. Note that when this approach to setting colours is used, any overplotting will revert to the colortable slot of the object, or the default for rasters, which is terrain.color()

cols can also accept RColorBrewer colors by keyword if it is character vector of length 1. i.e., this cannot be used to set many objects by keyword in the same Plot call. Default terrain.color(). See Details.

Some coloring will be automatic. If the object being plotted is a Raster, then this will take the colorTable slot (can be changed via setColors() or other ways). If this is a SpatialPointsDataFrame, this function will use a column called colors and apply these to the symbols.

Silently, one hidden object is made, .spadesPlot in the .spadesEnv environment, which is used for arranging plots in the device window, and identifying the objects to be replotted if rearranging is required, subsequent to a new = FALSE additional plot.

This function is optimized to allow modular Plotting. This means that several behaviours will appear unusual. For instance, if a first call to Plot is made, the legend will reflect the current color scheme. If a second or subsequent call to Plot is made with the same object but with different colours (e.g., with cols), the legend will not update. This behaviour is made with the decision that the original layer takes precedence and all subsequent plots to that same frame are overplots only.

speedup is not a precise number because it is faster to plot an un-resampled raster if the new resampling is close to the original number of pixels. At the moment, for rasters, this is set to 1/3 of the original pixels. In other words, speedup will not do anything if the factor for speeding up is not high enough (i.e., >3). If no sub-sampling is desired, use a speedup value less than 0.1.

These gp* parameters will specify plot parameters that are available with gpar(). gp will adjust plot parameters, gpText will adjust title and legend text, gpAxis will adjust the axes. size adjusts point size in a SpatialPoints object. These will persist with the original Plot call for each individual object. Multiple entries can be used, but they must be named list elements and they must match the ... items to plot. This is true for a RasterStack also, i.e., the list of named elements must be the same length as the number of layers being plotted. The naming convention used is: RasterStackName$layerName, i.e, landscape$DEM.

Value

Invisibly returns the .spadesPlot class object. If this is assigned to an object, say obj, then this can be plotted again with Plot(obj). This object is also stored in the locked .spadesEnv, so can simply be replotted with rePlot() or on a new device with rePlot(n), where n is the new device number.

See Also

clearPlot, gpar, raster, par, SpatialPolygons, grid.polyline, ggplot, dev

# @importClassesFrom NetLogoRClasses griddedClasses

Aliases
  • Plot
  • Plot,ANY-method
  • Plot,simList-method
  • rePlot
Examples
## Not run: 
# library(sp)
# library(raster)
# library(rgdal)
# library(igraph)
# library(RColorBrewer)
# # Make list of maps from package database to load, and what functions to use to load them
# filelist <-
#    data.frame(files =
#      dir(file.path(
#        find.package("SpaDES", quiet = FALSE), "maps"),
#        full.names = TRUE, pattern= "tif"),
#      functions = "rasterToMemory",
#      packages = "SpaDES",
#      stringsAsFactors = FALSE)
# 
# # Load files to memory (using rasterToMemory)
# mySim <- loadFiles(filelist = filelist)
# 
# # put layers into a single stack for convenience
# landscape <- stack(mySim$DEM, mySim$forestCover, mySim$forestAge,
#    mySim$habitatQuality, mySim$percentPine)
# 
# # can change color palette
# setColors(landscape, n = 50) <- list(DEM=topo.colors(50),
#                            forestCover = brewer.pal(9, "Set1"),
#                            forestAge = brewer.pal("Blues", n=8),
#                            habitatQuality = brewer.pal(9, "Spectral"),
#                            percentPine = brewer.pal("GnBu", n=8))
# 
# # Make a new raster derived from a previous one; must give it a unique name
# habitatQuality2 <- landscape$habitatQuality ^ 0.3
# names(habitatQuality2) <- "habitatQuality2"
# 
# # make a SpatialPoints object
# caribou <- cbind(x = stats::runif (1e2, -50, 50), y = stats::runif (1e2, -50, 50)) %>%
#   SpatialPoints(coords = .)
# 
# # use factor raster to give legends as character strings
# ras <- raster(matrix(sample(1:4, size=12, replace=TRUE),
#    ncol=4, nrow=3))
# # needs to have a data.frame with ID as first column - see ?raster::ratify
# levels(ras) <- data.frame(ID=1:4, Name=paste0("Level",1:4))
# if (interactive()) Plot(ras, new=TRUE)
# 
# # Arbitrary values for factors
# levels <- c(1,2,7)
# ras <- raster(matrix(sample(levels, size=12, replace=TRUE),
#    ncol=4, nrow=3))
# levels(ras) <- data.frame(ID=levels, Name=sample(LETTERS,3))
# 
# # SpatialPolygons
# Sr1 = Polygon(cbind(c(2, 4, 4, 1, 2), c(2, 3, 5, 4, 2))*20-50)
# Sr2 = Polygon(cbind(c(5, 4, 2, 5), c(2, 3, 2, 2))*20 - 50)
# Srs1 = Polygons(list(Sr1), "s1")
# Srs2 = Polygons(list(Sr2), "s2")
# SpP = SpatialPolygons(list(Srs1, Srs2), 1:2)
# 
# if (interactive()) {
#   Plot(ras, new = TRUE)
# 
#   # dev(2)
# 
#   Plot(landscape, new = TRUE)
# 
#   # Can overplot, using addTo
#   Plot(caribou, addTo = "landscape$forestAge", size = 4, axes = FALSE)
# 
#   # can add a plot to the plotting window
#   Plot(caribou, new = FALSE)
# 
#   # Can add two maps with same name, if one is in a stack; they are given
#   #  unique names based on object name
#   Plot(landscape, caribou, mySim$DEM)
# 
#   # can mix stacks, rasters, SpatialPoint*
#   Plot(landscape, habitatQuality2, caribou)
# 
#   # can mix stacks, rasters, SpatialPoint*, and SpatialPolygons*
#   Plot(landscape, caribou)
#   Plot(habitatQuality2, new = FALSE)
#   Plot(SpP)
#   Plot(SpP, addTo = "landscape$forestCover", gp = gpar(lwd = 2))
# }
# 
# ## End(Not run)

Documentation reproduced from package SpaDES, version 1.2.0, License: GPL-3

Community examples

Looks like there are no examples yet.