[R] How to plot soil moisture data as a contour plot

[David Winsemius]

On Sep 10, 2014, at 1:20 PM, Thiago V. dos Santos wrote:

> Dear all,
> 
> This is my first message in this list, so please excuse any mistake.
> 
> I am trying to plot moisture data for 11 soil layers over the course of the year, but I am yet to find the correct function to do that. I am trying to reproduce the lower figure in this panel: https://imageshack.com/i/exmVz5QSp
> 
> Please read the comments while reproducing my data with the code below: 
> 
> ----------------------------------------
> library(repmis) # reads text data directly from dropbox - no need to download any file
> 
> # read data
> url <- 'https://dl.dropboxusercontent.com/u/27700634/precip.txt'
> tmp <- repmis::source_data(url, sep = '', header = TRUE)
> 
> # convert julian day to date
> date <- as.Date(tmp$julian, origin='2011-12-31')
> data <- cbind(date, tmp)
> head(data)
> 
> # now, convert soil layers to matrix and transpose it
> mat <- t(as.matrix(data[, 4:14]))
> head(mat) 
> 
> # this is the very matrix I want to plot. Please notice that it is already organized as a "profile",
> # with rows representing soil layers and columns representing day of year.
> ----------------------------------------
> 
> 
> My first attempt was to use function filled.contour from "graphics" package. I define a vector with labels for soil layers and then I try to plot, but I receive an error saying the matrix has incorrect dimensions:
> 
> 
> ----------------------------------------
> 
> # define vector with depth of soil layers
> 
> depths <- c(0.05,0.10,0.20,0.30,
>            0.40,0.60,0.80,1.00,
>            1.50,2.00,2.50)
> 
> # Plot soil moisture profile
> plot <- filled.contour(data$julian, depths, mat)
> 
> 
> #Error in .filled.contour(x, y, z, levels, col) : dimension mismatch

You need to decide what orientation you want. At the moment the mat-matrix is 11 x 366 and the x-component is the 11. (And for some reason you are the one who made the first transposition.) There's no auto-transformation in filled.contour when the dimensions are reversed. 

This proceeds without error:

mat2 <- as.matrix(data[, 4:14])
plot <- filled.contour(x=data$julian, y=depths, z=mat2)

> ----------------------------------------
> 
> 
> I can obviously tranpose the matrix to force the plot, but the resulting figure is not what I need - the soil profile is shown upside down:
> 

If you want the reverse the depth order, do not transpose, .... just:

plot <- filled.contour(x=data$julian, y=depths, z=mat2[, 11:1])



> ----------------------------------------
> plot <- filled.contour(data$julian, depths, t(mat))
> 
> ----------------------------------------
> 
> 
> Because this functions requires axis labels to be ascendent, I am not able to reverse them in order to show the first layer at the top of the graphic.
> 
> I would really appreciate any feedback or directions on how to show my data as a contour plot as mentioned above. Thanks in advance! 
> 
> 
> Greetings,
> --
> Thiago V. dos Santos
> PhD student
> Land and Atmospheric Science
> University of Minnesota
> http://www.laas.umn.edu/CurrentStudents/MeettheStudents/ThiagodosSantos/index.htm
> Phone: (612) 323
> 9898
> 	[[alternative HTML version deleted]]
> 
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David Winsemius
Alameda, CA, USA