R help - Sep 2014 - How to plot soil moisture data as a contour plot

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
----------------------------------------


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:

----------------------------------------
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]]

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]]
> 
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
David Winsemius
Alameda, CA, USA