Depth Profiling visualization

Question

I'm trying to create a depth profile graph with the variables depth, distance and temperature. The data collected is from 9 different points with known distances between them (distance 5m apart, 9 stations, 9 different sets of data). The temperature readings are according to these 9 stations where a sonde was dropped directly down, taking readings of temperature every 2 seconds. Max depth at each of the 9 stations were taken from the boat also.

So the data I have is:

1. Depth at each of the 9 stations (y axis)
2. Temperature readings at each of the 9 stations, at around .2m intervals vertical until the bottom was reached (fill area)
3. distance between the stations, (x axis)

Is it possible to create a depth profile similar to this? (obviously without the greater resolution in this graph)

I've already tried messing around with ggplot2 and raster but I just can't seem to figure out how to do this. One of the problems I've come across is how to make ggplot2 distinguish between say 5m depth temperature reading at station 1 and 5m temperature reading at station 5 since they have the same depth value.

Even if you can guide me towards another program that would allow me to create a graph like this, that would be great

Answer 1

[ REVISION ]
(Please comment me if you know more suitable interpolation methods, especially not needing to cut under bottoms data.)

ggplot() needs long data form.

library(ggplot2)

# example data
max.depths <- c(1.1, 4, 4.7, 7.7, 8.2, 7.8, 10.7, 12.1, 14.3)
depth.list <- sapply(max.depths, function(x) seq(0, x, 0.2))
temp.list <- list()
set.seed(1); for(i in 1:9) temp.list[[i]] <- sapply(depth.list[[i]], function(x) rnorm(1, 20 - x*0.5, 0.2))
set.seed(1); dist <- c(0, sapply(seq(5, 40, 5), function(x) rnorm(1, x, 1)))
dist.list <- sapply(1:9, function(x) rep(dist[x], length(depth.list[[x]])))

main.df <- data.frame(dist = unlist(dist.list), depth = unlist(depth.list) * -1, temp = unlist(temp.list))

# a raw graph
ggplot(main.df, aes(x = dist, y = depth, z = temp)) + 
  geom_point(aes(colour = temp), size = 1) +
  scale_colour_gradientn(colours = topo.colors(10))

# a relatively raw graph   (don't run with this example data)
ggplot(main.df, aes(x = dist, y = depth, z = temp)) + 
  geom_raster(aes(fill = temp)) + # geom_contour() +
  scale_fill_gradientn(colours = topo.colors(10))

If you want a graph such like you showed, you have to do interpolation. Some packages give you spatial interpolation methods. In this example, I used akima package but you should think seriously that which interpolation methods to use.

I used nx = 300 and ny = 300 in below code but I think it would be better to decide those values carefully. Large nx and ny gives a high resolution graph, but don't foreget real nx and ny (in this example, real nx is only 9 and ny is 101).

library(akima); library(dplyr)

interp.data <- interp(main.df$dist, main.df$depth, main.df$temp, nx = 300, ny = 300)
interp.df <- interp.data %>% interp2xyz() %>% as.data.frame()
names(interp.df) <- c("dist", "depth", "temp")

# draw interp.df
ggplot(interp.df, aes(x = dist, y = depth, z = temp)) + 
  geom_raster(aes(fill = temp)) + # geom_contour() +
  scale_fill_gradientn(colours = topo.colors(10))

# to think appropriateness of interpolation (raw and interpolation data)
ggplot(interp.df, aes(x = dist, y = depth, z = temp)) + 
  geom_raster(aes(fill = temp), alpha = 0.3) +                 # interpolation
  scale_fill_gradientn(colours = topo.colors(10)) + 
  geom_point(data = main.df, aes(colour = temp), size = 1) +  # raw
  scale_colour_gradientn(colours = topo.colors(10))

Bottoms don't match !!
I found ?interp says "interpolation only within convex hull!", oops... I'm worrid about the interpolation around the problem-area, is it OK ? If no problem, you need only cut the data under the bottoms. If not, ... I can't answer immediately (below is an example code to cut).

bottoms <- max.depths * -1

# calculate bottom values using linear interpolation
approx.bottoms <- approx(dist, bottoms, n = 300) # n must be the same value as interp()'s nx

# change temp values under bottom into NA
library(dplyr)
interp.cut.df <- interp.df %>% cbind(bottoms = approx.bottoms$y) %>% 
  mutate(temp = ifelse(depth >= bottoms, temp, NA)) %>% select(-bottoms)

ggplot(interp.cut.df, aes(x = dist, y = depth, z = temp)) + 
  geom_raster(aes(fill = temp)) + 
  scale_fill_gradientn(colours = topo.colors(10)) + 
  geom_point(data = main.df, size = 1)

If you want to use stat_contour
It is harder to use stat_contour than geom_raster because it needs a regular grid form. As far as I see your graph, your data (depth and distance) don't form a regular grid, it means it is much difficult to use stat_contour with your raw data. So I used interp.cut.df to draw a contour plot. And stat_contour have a endemic problem (see How to fill in the contour fully using stat_contour), so you need to expand your data.

library(dplyr)

# 1st: change NA into a temp's out range value (I used 0)
interp.contour.df <- interp.cut.df
interp.contour.df[is.na(interp.contour.df)] <- 0

# 2nd: expand the df (It's a little complex, so please use this function)
contour.support.func <- function(df) {
  colname <- names(df)
  names(df) <- c("x", "y", "z")
  Range <- as.data.frame(sapply(df, range))
  Dim <- as.data.frame(t(sapply(df, function(x) length(unique(x)))))
  arb_z = Range$z[1] - diff(Range$z)/20
  df2 <- rbind(df,
               expand.grid(x = c(Range$x[1] - diff(Range$x)/20, Range$x[2] + diff(Range$x)/20), 
                           y = seq(Range$y[1], Range$y[2], length = Dim$y), z = arb_z),
               expand.grid(x = seq(Range$x[1], Range$x[2], length = Dim$x),
                           y = c(Range$y[1] - diff(Range$y)/20, Range$y[2] + diff(Range$y)/20), z = arb_z))
 names(df2) <- colname
 return(df2)
}

interp.contour.df2 <- contour.support.func(interp.contour.df)

# 3rd: check the temp range (these values are used to define contour's border (breaks))
range(interp.cut.df$temp, na.rm=T)        # 12.51622 20.18904

# 4th: draw ... the bottom border is dirty !!
ggplot(interp.contour.df2, aes(x = dist, y = depth, z = temp)) + 
  stat_contour(geom="polygon", breaks = seq(12.51622, 20.18904, length = 11), aes(fill = ..level..)) + 
  coord_cartesian(xlim = range(dist), ylim = range(bottoms), expand = F) + # cut expanded area
  scale_fill_gradientn(colours = topo.colors(10)) # breaks's length is 11, so 10 colors are needed

# [Note]
# You can define the contour's border values (breaks) and colors.
contour.breaks <- c(12.5, 13.5, 14.5, 15.5, 16.5, 17.5, 18.5, 19.5, 20.5) 
    # = seq(12.5, 20.5, 1) or seq(12.5, 20.5, length = 9)
contour.colors <- c("darkblue", "cyan3", "cyan1", "green3", "green", "yellow2","pink", "darkred")
   # breaks's length is 9, so 8 colors are needed.

# 5th: vanish the bottom border by bottom line
approx.df <- data.frame(dist = approx.bottoms$x, depth = approx.bottoms$y, temp = 0)  # 0 is dummy value

ggplot(interp.contour.df2, aes(x = dist, y = depth, z = temp)) + 
  stat_contour(geom="polygon", breaks = contour.breaks, aes(fill = ..level..)) +
  coord_cartesian(xlim=range(dist), ylim=range(bottoms), expand = F) + 
  scale_fill_gradientn(colours = contour.colors) +
  geom_line(data = approx.df, lwd=1.5, color="gray50")

bonus: legend technic

library(dplyr)
interp.contour.df3 <- interp.contour.df2 %>% mutate(temp2 = cut(temp, breaks = contour.breaks))
interp.contour.df3$temp2 <- factor(interp.contour.df3$temp2, levels = rev(levels(interp.contour.df3$temp2)))

ggplot(interp.contour.df3, aes(x = dist, y = depth, z = temp)) + 
  stat_contour(geom="polygon", breaks = contour.breaks, aes(fill = ..level..)) +
  coord_cartesian(xlim=range(dist), ylim=range(bottoms), expand = F) + 
  scale_fill_gradientn(colours = contour.colors, guide = F) +   # add guide = F
  geom_line(data = approx.df, lwd=1.5, color="gray50") +
  geom_point(aes(colour = temp2), pch = 15, alpha = 0) +        # add
  guides(colour = guide_legend(override.aes = list(colour = rev(contour.colors), alpha = 1, cex = 5))) +  # add
  labs(colour = "temp")   # add