plot.bathy {marmap}

Ploting bathymetric data

Description

Plots contour map from bathymetric data matrix of class bathy

Usage

## S3 method for class '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, ...)

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.

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).

Value

a bathymetric map with isobaths

Note

plot.bathy uses a matrix of class bathy, and can therefore be substituted for plot.

Author(s)

Eric Pante and Benoit Simon-Bouhet

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

See Also

read.bathy, summary.bathy, nw.atlantic, metallo

Examples

# 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")))