Last chance! 50% off unlimited learning
Sale ends in
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, \dots)bathy, imported using read.bathyFALSE)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)bathy dataset (default is FALSE)n isobaths are automatically plotted within the depth range of the bathy matrix (default is 20).TRUE, a color for the area of the matrix not bracketed by the list supplied to bpal (see below; default is white)FALSE); may contain several elementsplot.windowcountour (default) or to image when argument image=TRUE.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).
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
on 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")))Run the code above in your browser using DataLab