plot.bathy: Ploting bathymetric data

Description

Plots contour map from bathymetric data matrix of class bathy

Usage

# S3 method for bathy
plot(x, image=FALSE, bpal=NULL, land=FALSE,
           deepest.isobath, shallowest.isobath, step, n=20,
           lwd=1, lty=1, col="black", default.col="white", drawlabels = FALSE,
           xlab="Longitude", ylab="Latitude", asp=1, ...)

Value

a bathymetric map with isobaths

Arguments

x: bathymetric data matrix of class bathy, imported using read.bathy
image: whether or not to color depth layers (default is FALSE)
bpal: if image is TRUE, either NULL (default: a simple blue color palette is used), a vector of colors, or a list of depth bounds and colors (see below)
land: whether or not to use topographic data that may be available in the bathy dataset (default is FALSE)
deepest.isobath: deepest isobath(s) to plot
shallowest.isobath: shallowest isobath(s) to plot
step: distance(s) between two isobaths
n: if the user does not specify the range within which isobaths should be plotted, about n isobaths are automatically plotted within the depth range of the bathy matrix (default is 20).
lwd: isobath line(s) width (default is 1)
lty: isobath line type(s) (default is 1)
col: isobath line color(s) (default is black)
default.col: if image is TRUE, a color for the area of the matrix not bracketed by the list supplied to bpal (see below; default is white)
drawlabels: whether or not to plot isobath depth as a label (default is FALSE); may contain several elements
xlab: label for the x axis of the plot
ylab: label for the y axis of the plot
asp: numeric, giving the aspect ratio y/x of the plot. See plot.window
...: Other arguments to be passed either to countour (default) or to image when argument image=TRUE.

Author

Eric Pante and Benoit Simon-Bouhet

Details

plot.bathy uses the base contour and image functions. If a vector of isobath characteristics is provided, different types of isobaths can be added to the same plot using a single call of plot.bathy (see examples)

If image=TRUE, the user has three choices for colors: (1) bpal can be set to NULL, in which case a default blue color palette is generated; (2) colors can be user-defined as in example 4, in which case the palette can be generated with function colorRampPalette (colors are then supplied as a vector to plot.bathy) ; (3) colors can be constrained to bathymetry- and/or topography. In this last case, a list of vectors is supplied to plot.bathy (example 7): each vector corresponds to a bathymetry/topography layer (for example, one layer for bathymetry and one layer for topography). The first and second elements of the vector are the minimum and maximum bathymetry/topography, respectively. The other elements of the vector (3, onward) correspond to colors (see example 7).

References

Eric Pante, Benoit Simon-Bouhet (2013) marmap: A Package for Importing, Plotting and Analyzing Bathymetric and Topographic Data in R. PLoS ONE 8(9): e73051. doi:10.1371/journal.pone.0073051. https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0073051

Examples

Run this code

# load NW Atlantic data and convert to class bathy
	data(nw.atlantic)
	atl <- as.bathy(nw.atlantic)

## Example 1: a simple marine chart
	plot(atl) # without specifying any isobath parameters
	plot(atl, n=5, drawlabels=TRUE) # with about 5 isobaths
	plot(atl, deep=-8000, shallow=0, step=1000) # with isobath parameters

## Example 2: taking advantage of multiple types of isobaths
	plot(atl, deep=c(-8000,-2000,0), shallow=c(-2000,-100,0), step=c(1000,100,0),
		 lwd=c(0.5,0.5,1),lty=c(1,1,1),col=c("grey80","red", "blue"),
		 drawlabels=c(FALSE,FALSE,FALSE) )

## Example 3: plotting a colored map with the default color palette
	plot(atl, image=TRUE, deep=c(-8000,0), shallow=c(-1000,0), step=c(1000,0),
	     lwd=c(0.5,1), lty=c(1,1), col=c("grey","black"), drawlabels=c(FALSE,FALSE))

## Example 4: make a pretty custom color ramp
	colorRampPalette(c("purple","lightblue","cadetblue2","cadetblue1","white")) -> blues

	plot(atl, image=TRUE, bpal=blues(100), deep=c(-6500,0), shallow=c(-50,0), step=c(500,0),
	     lwd=c(0.3,1), lty=c(1,1), col=c("black","black"), drawlabels=c(FALSE,FALSE))

	scaleBathy(atl, deg=3, x="bottomleft", inset=5)

## Example 5: add points corresponding to sampling locations
##            point colors correspond to the sampling depth
	par(mai=c(1,1,1,1.5))
	plot(atl, deep=c(-4500,0), shallow=c(-50,0), step=c(500,0),
	     lwd=c(0.3,1), lty=c(1,1), col=c("black","black"), drawlabels=c(FALSE,FALSE))

	# add a title to the plot
	title(main="Distribution of coral samples\non the New England and Corner Rise seamounts")
	# add a scale
	scaleBathy(atl, deg=3, x="bottomleft", inset=5)

	# add a geographical reference on the coast:
	points(-71.064,42.358, pch=19)
	text(-71.064,42.358,"Boston", adj=c(1.2,0))

	# prepare colors for the sampling locations:
	data(metallo) ## see dataset metallo
	max(metallo$depth, na.rm=TRUE) -> mx
	colorRampPalette(c("white","lightyellow","lightgreen","blue","lightblue1","purple")) -> ramp
	blues <- ramp(max(metallo$depth))

	# plot sampling locations:
	points(metallo, col="black", bg=blues[metallo$depth], pch=21,cex=1.5)
	library(shape)
	colorlegend(zlim=c(-mx,0), col=rev(blues), main="depth (m)",posx=c(0.85,0.88))

## Example 6: use packages maps and mapdata in combination with marmap
	# use maps and mapdata to plot the coast
	library(maps)
	library(mapdata)
	map('worldHires',xlim=c(-75,-46),ylim=c(32,44), fill=TRUE, col="grey")
	box();axis(1);axis(2)

	# add bathymetric data from 'bathy' data
    plot(atl, add=TRUE, lwd=.3, deep=-4500, shallow=-10, step=500,
		drawlabel=FALSE, col="grey50")

## Example 7: provide a list of depths and colors to argument bpal to finely tune palette
	# check out ?palette.bathy to see details on how the palette is handled

	# creating depth-constrained palette for the ocean only
	plot(atl, land = FALSE, n = 10, lwd = 0.5, image = TRUE,
	     bpal = list(c(min(atl), 0, "purple", "blue", "lightblue")),
	     default.col = "gray")

	# creating depth-constrained palette for 3 ocean "layers"
	plot(atl, land = FALSE, n = 10, lwd = 0.7, image = TRUE,
	     bpal = list(c(min(atl), -3000, "purple","blue","grey"),
	                 c(-3000, -150, "white"),
	                 c(-150, 0, "yellow", "green", "brown")),
	     default.col = "grey")

	# creating depth-constrained palette for land and ocean
	plot(atl, land = TRUE, n = 10, lwd = 0.7, image = TRUE,
	     bpal = list(c(min(atl), 0, "purple", "blue", "lightblue"),
	                 c(0, max(atl), "gray90", "gray10")))

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