plot.bathy | R Documentation |
Plots contour map from bathymetric data matrix of class bathy
## 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, ...)
x |
bathymetric data matrix of class |
image |
whether or not to color depth layers (default is |
bpal |
if image is |
land |
whether or not to use topographic data that may be available in the |
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 |
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 |
drawlabels |
whether or not to plot isobath depth as a label (default is |
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 |
... |
Other arguments to be passed either to |
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).
a bathymetric map with isobaths
plot.bathy
uses a matrix of class bathy
, and can therefore be substituted for plot
.
Eric Pante and Benoit Simon-Bouhet
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
read.bathy
, summary.bathy
, nw.atlantic
, metallo
# 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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