David
A function to draw an oceanographic section of interpolated data along a
transect. Requires packages sp, marmap, MBA, reshape2, and
ggplot2.
longitude – vector of latitude in degrees north
latitude – vector of longitude in degrees east
parameter – vector of values of parameter z to be interpolated and plotted as color; accepts NAs but all Lon-Lat-Depth-Parameter combinations with parameters NA will be removed
depth – vector of depth values in m, negative numbers are accepted but will be converted to positives
xy.ratio = NULL – optional integer vector of length 2 in which first and second integers indicate the relative strength of interpolation in x and y direction, defaults to NULL and calculates the required values according to mean depth resolution and distance between stations
section.x = “km” – unit for x axis of the section; options are “km” (the default), “degE”, and “degN”
section.direction = NA – optional sorting of data by stations along a dominant direction. Options are “N”, “E”, “S”, and “W”, e.g. “S” creates a section running from north to south. If nothing is input, data vectors will not be resorted
bathymetry = NULL – optional bathymetry of class “bathy”, if not supplied will be retrieved from NOAA for the domain of “longitude” and “latitude”
keep.bathy = FALSE – should the downloaded bathymetry be kept offline; this would make repeated plotting faster
max.depth = “profile” – select the section’s maximum depth in bathymetry (“profile”, the default) or in data (“data”) as the maximum depth of the plot
contour.breaks = 5 – either an integer defining the number of contour bins (defaults arbitrarily to 5), or a vector of values for the contour lines.
A named list containing the $plot, the $input data with the distance of stations along the section (according to sorting via section.direction), the $output data of the interpolated results (as a long table), and the $profile of bathymetry under the section.
The example data from the Black Sea is available for download from PANGEA. Because the downloaded data is not sorted properly, the general cruise direction from west to east is indicated by section.direction = “E”.
data <- read.table("Kaiser-etal_MSM33.tab", sep = "\t", skip = 99, header = TRUE)
example <- section(longitude = data$Longitude,
latitude = data$Latitude,
parameter = data$Sal,
depth = data$Depth.water..m.,
section.direction = "E")example$plot 
Because the $plot is a ggplot2 object, it can be modified and extended.
example$plot +
coord_cartesian(ylim=c(500,0)) +
metR::geom_label_contour(data = example$output,
aes(section.x, depth, z = parameter)) +
scale_fill_gradientn(colours = c("black", "grey", "white"), name = "salinity")
The other objects in the results list are simple data frames.
head(example$input)## longitude latitude parameter depth section.x
## 1 31.1403 45.02997 17.2305 1.5 0.00000000
## 2 31.1403 45.03010 17.2497 10.0 0.01444735
## 3 31.1403 45.03010 17.4900 20.0 0.01444735
## 4 31.1403 45.03010 17.8401 30.0 0.01444735
## 5 31.1403 45.03020 17.8487 32.5 0.02556070
## 6 31.1403 45.03020 18.2096 40.0 0.02556070
head(example$output)## section.x depth parameter
## 1 0.000000 1.5 17.20472
## 2 2.116863 1.5 17.23667
## 3 4.233726 1.5 17.30980
## 4 6.350589 1.5 17.39558
## 5 8.467452 1.5 17.48017
## 6 10.584315 1.5 17.55927
head(example$profile)## lon lat section.x depth
## 2 31.13370 45.02793 0.000000 31
## 6 31.14943 45.01117 2.236433 25
## 7 31.16516 44.99441 4.473066 28
## 8 31.18089 44.97765 6.709898 33
## 9 31.19662 44.96089 8.946931 29
## 10 31.21235 44.94413 11.184163 22