Re: [R] Soil texture triangle in R?

From: Sander Oom <slist_at_oomvanlieshout.net>
Date: Sat 28 May 2005 - 06:27:37 EST

Cleaned up the class divisions and created a full function.

Still to do:

- rotate axis labels;
- correct the partial covering of the bottom tick labels;
- rotate ticks in order to simplify viewing the graph.
See:
http://soil.scijournals.org/content/vol65/issue4/images/large/1038f2.jpeg

Wonder whether triangle.plot{ade4} will give more flexibility!?

Anyway, hopefully the result so far is useful for other people.

Cheers,

Sander.

plot.soiltexture <- function(x,pch,col) {

   ## triangle plots:
   ##   triangle.plot {ade4}
   ##   triplot{klaR}
   ##   ternaryplot {vcd}

   require(vcd)
   require(Zelig)
   ternaryplot(x,
     grid=FALSE,
     dimnames.position = "none",
     pch=pch, col=col,
     scale=1, main=NULL,
     prop.size=FALSE

   )
   oldpar <- par(no.readonly=TRUE)

   ticlength <- 0.01
   ## now the bottom internal ticks

   x1<-seq(0.1,0.9,by=0.1)
   x2<-x1
   y1<-rep(0,9)
   y2<-rep(ticlength,9)

   segments(x1,y1,x2,y2)
   text(x1,y1-0.03,as.character(rev(seq(10,90,by=10)))) #, cex=0.8)    ## now the left internal ticks
   y1<-x1*sin60
   x1<-x1*0.5
   x2<-x1+ticlength*sin60
   y2<-y1-ticlength*0.5

   segments(x1,y1,x2,y2)
   text(x1-0.03,y1+0.015,as.character(seq(10,90,by=10)))    ## now the right internal ticks
   x1<-rev(x1+0.5-ticlength*sin60)
   x2<-x1+ticlength*sin60
   segments(x1,y2,x2,y1)
   text(x2+0.03,y1+0.015,as.character(rev(seq(10,90,by=10))))

   ## the labels at the corners
   par(xpd=TRUE)

#   text(0.5,0.9,"100% clay")
#   text(-0.1,0,"100% sand")
#   text(1.1,0,"100% loam")

   ## the axis labels

   text(0.09,0.43,"% Clay")
   text(0.90,0.43,"% Silt")
   text(0.5,-0.1,"% Sand")

   # boundary of clay with extensions

   x1<-c(0.275,0.355,0.6)
   x2<-c(0.415,0.8,0.7)
   y1<-c(0.55*sin60,0.4*sin60,0.4*sin60)
   y2<-c(0.285*sin60,0.4*sin60,0.6*sin60)
   segments(x1,y1,x2,y2, col="grey")
   text(0.5,0.57,"Clay", col="grey")
   # lower bound of clay loam & silty divider
   x1<-c(0.415,0.66)
   x2<-c(0.856,0.6)
   y1<-c(0.285*sin60,0.285*sin60)
   y2<-c(0.285*sin60,0.40*sin60)

   segments(x1,y1,x2,y2, col="grey")
   text(0.7,0.49*sin60,"Silty", col="grey")
   text(0.7,0.44*sin60,"clay", col="grey")
   text(0.72,0.36*sin60,"Silty clay", col="grey")
   text(0.73,0.32*sin60,"loam", col="grey")
   text(0.5,0.35*sin60,"Clay loam", col="grey")
   x1<-c(0.185,0.1,0.37)
   x2<-c(0.37,0.37,0.415)

   y1<-c(0.37*sin60,0.2*sin60,0.2*sin60)    y2<-c(0.37*sin60,0.2*sin60,0.285*sin60)
   segments(x1,y1,x2,y2, col="grey")
   text(0.28,0.43*sin60,"Sandy", col="grey")
   text(0.27,0.39*sin60,"clay", col="grey")
   text(0.27,0.3*sin60,"Sandy clay", col="grey")    text(0.27,0.26*sin60,"loam", col="grey")    # sand corner
   x1<-c(0.05,0.075)
   x2<-c(0.15,0.3)
   y1<-c(0.1*sin60,0.15*sin60)
   y2<-c(0,0)
   segments(x1,y1,x2,y2, col="grey")
   text(0.25,0.13*sin60,"Sandy loam", col="grey")
   text(0.14,0.07*sin60,"Loamy", col="grey")
   text(0.18,0.03*sin60,"sand", col="grey")    text(0.06,0.021,"Sand", col="grey")
   x1<-c(0.37,0.435,0.5,0.8,0.86)
   x2<-c(0.435,0.537,0.64,0.86,0.94)
   y1<-c(0.2*sin60,0.08*sin60,0,0,0.12*sin60)
   y2<-c(0.08*sin60,0.08*sin60,0.285*sin60,0.12*sin60,0.12*sin60)
   segments(x1,y1,x2,y2, col="grey")
   text(0.49,0.18*sin60,"Loam", col="grey")
   text(0.72,0.15*sin60,"Silt loam", col="grey")    text(0.9,0.06*sin60,"Silt", col="grey")

   ternarypoints(x, pch = pch, col = col)

   par(oldpar)
}

tmp <- array(dim=c(10,3))
tmp[,2] <- abs(rnorm(10)*20)
tmp[,3] <- abs(rnorm(10)*10)

tmp[,1] <- 100-tmp[,2]-tmp[,3]
col <- rep("black",10)
pch <- rep(1, 10)
plot.soiltexture(tmp,pch,col="black")

Sander Oom wrote:
> Right,
>
> Got the data points plotted on top of the soil texture background,
> thanks to Jim and ternaryplot{vcd}! See code below.
>
> Now there is some fine tuning to do, as it should really look like this
> graph:
> http://soil.scijournals.org/content/vol65/issue4/images/large/1038f2.jpeg
>
> Things to do:
> - rotate axis labels;
> - correct small errors in class divisions;
> - correct the partial covering of the bottom tick labels;
> - rotate ticks in order to simplify viewing the graph.
>
> Any help still appreciated!
>
> Cheers,
>
> Sander.
>
>
> soil.triangle <- function() {
> oldpar <- par(no.readonly=TRUE)
> ## now the bottom internal ticks
> x1<-seq(0.1,0.9,by=0.1)
> x2<-x1
> y1<-rep(0,9)
> y2<-rep(-0.02,9)
> segments(x1,y1,x2,y2)
> text(x1,y1-0.03,as.character(rev(seq(10,90,by=10)))) #, cex=0.8)
> ## now the left internal ticks
> y1<-x1*sin60
> x1<-x1*0.5
> x2<-x1+0.02*sin60
> y2<-y1-0.02*0.5
> segments(x1,y1,x2,y2)
> text(x1-0.03,y1+0.015,as.character(seq(10,90,by=10)))
> ## now the right internal ticks
> x1<-rev(x1+0.5-0.02*sin60)
> x2<-x1+0.02*sin60
> segments(x1,y2,x2,y1)
> text(x2+0.03,y1+0.015,as.character(rev(seq(10,90,by=10))))
> ## the labels at the corners
> par(xpd=TRUE)
> # text(0.5,0.9,"100% clay")
> # text(-0.1,0,"100% sand")
> # text(1.1,0,"100% loam")
> text(0.09,0.43,"% Clay")
> text(0.90,0.43,"% Silt")
> text(0.5,-0.1,"% Sand")
> # boundary of clay with extensions
> x1<-c(0.275,0.35,0.6)
> x2<-c(0.4,0.79,0.7)
> y1<-c(0.55*sin60,0.41*sin60,0.41*sin60)
> y2<-c(0.285*sin60,0.41*sin60,0.6*sin60)
> segments(x1,y1,x2,y2, col="grey")
> text(0.5,0.57,"Clay", col="grey")
> # lower bound of clay loam & silty divider
> x1<-c(0.4,0.68)
> x2<-c(0.86,0.6)
> y1<-c(0.285*sin60,0.285*sin60)
> y2<-c(0.285*sin60,0.41*sin60)
> segments(x1,y1,x2,y2, col="grey")
> text(0.7,0.49*sin60,"Silty", col="grey")
> text(0.7,0.44*sin60,"clay", col="grey")
> text(0.73,0.37*sin60,"Silty clay", col="grey")
> text(0.73,0.33*sin60,"loam", col="grey")
> text(0.5,0.35*sin60,"Clay loam", col="grey")
> x1<-c(0.185,0.1,0.37)
> x2<-c(0.36,0.37,0.4)
> y1<-c(0.37*sin60,0.2*sin60,0.2*sin60)
> y2<-c(0.37*sin60,0.2*sin60,0.285*sin60)
> segments(x1,y1,x2,y2, col="grey")
> text(0.27,0.43*sin60,"Sandy", col="grey")
> text(0.27,0.39*sin60,"clay", col="grey")
> text(0.27,0.3*sin60,"Sandy clay", col="grey")
> text(0.27,0.26*sin60,"loam", col="grey")
> # sand corner
> x1<-c(0.05,0.075)
> x2<-c(0.12,0.3)
> y1<-c(0.1*sin60,0.15*sin60)
> y2<-c(0,0)
> segments(x1,y1,x2,y2, col="grey")
> text(0.25,0.13*sin60,"Sandy loam", col="grey")
> text(0.13,0.075*sin60,"Loamy", col="grey")
> text(0.15,0.035*sin60,"sand", col="grey")
> text(0.055,0.021,"Sand", col="grey")
> x1<-c(0.37,0.42,0.5,0.8,0.86)
> x2<-c(0.42,0.54,0.65,0.86,0.94)
> y1<-c(0.2*sin60,0.08*sin60,0,0,0.12*sin60)
> y2<-c(0.08*sin60,0.08*sin60,0.285*sin60,0.12*sin60,0.12*sin60)
> segments(x1,y1,x2,y2, col="grey")
> text(0.49,0.18*sin60,"Loam", col="grey")
> text(0.72,0.15*sin60,"Silt loam", col="grey")
> text(0.9,0.06*sin60,"Silt", col="grey")
> par(oldpar)
> }
>
> tmp <- array(dim=c(10,3))
> tmp[,1] <- abs(rnorm(10)*20)
> tmp[,2] <- abs(rnorm(10)*10)
> tmp[,3] <- 100-tmp[,1]-tmp[,2]
> tmp
>
> library(vcd)
> ## Mark groups
> ternaryplot(tmp,
> grid=FALSE,
> dimnames.position = "none",
> pch=1, col="black",
> scale=1, main=NULL,
> prop.size=FALSE,
> )
> soil.triangle()
>
>
> Sander Oom wrote:

>> Hi Jim,
>>
>> This looks impressive! It gives me the 'background' graph. However, 
>> I'm not sure how I can use this function to plot my soil texture 
>> values! Can you explain?
>>
>> I would like to be able to plot my soil texture samples in the same 
>> graph as the one your function plots.
>>
>> Maybe I should try to figure out how to replicate your code inside a 
>> ternaryplot{vcd} call.
>>
>> Cheers,
>>
>> Sander.
>>
>> Jim Lemon wrote:
>>  > Sander Oom wrote:
>>  >> Dear R users,
>>  >>
>>  >> has anybody made an attempt to create the soil texture triangle graph
>>  >> in R? For an example see here:
>>  >>
>>  >> http://www.teachingkate.org/images/soiltria.gif
>>  >>
>>  >> I would like to get the lines in black and texture labels in gray to
>>  >> allow for plotting my texture results on top.
>>  >>
>>  >> Any examples or suggestions are very welcome!
>>  >>
>>  > It's not too hard to write a plot function to do this, but I'm not 
>> sure
>>  > whether this will be what you want. Anyway, try it out.
>>  >
>>  > Jim
>>  >
>>  > 
>> ------------------------------------------------------------------------
>>  >
>>  > soil.triangle<-function() {
>>  >  oldpar<-par(no.readonly=TRUE)
>>  >  plot(0:1,type="n",axes=FALSE,xlim=c(0,1.1),ylim=c(0,1),
>>  >   main="Soil Triangle",xlab="",ylab="")
>>  >  # first draw the triangle
>>  >  x1<-c(0,0,0.5)
>>  >  sin60<-sin(pi/3)
>>  >  x2<-c(1,0.5,1)
>>  >  y1<-c(0,0,sin60)
>>  >  y2<-c(0,sin60,0)
>>  >  segments(x1,y1,x2,y2)
>>  >  # now the bottom internal ticks
>>  >  x1<-seq(0.1,0.9,by=0.1)
>>  >  x2<-x1
>>  >  y1<-rep(0,9)
>>  >  y2<-rep(0.02,9)
>>  >  segments(x1,y1,x2,y2)
>>  >  text(x1,y1-0.03,as.character(rev(seq(10,90,by=10))))
>>  >  # now the left internal ticks
>>  >  y1<-x1*sin60
>>  >  x1<-x1*0.5
>>  >  x2<-x1+0.02*sin60
>>  >  y2<-y1-0.02*0.5
>>  >  segments(x1,y1,x2,y2)
>>  >  text(x1-0.03,y1+0.015,as.character(seq(10,90,by=10)))
>>  >  x1<-rev(x1+0.5-0.02*sin60)
>>  >  x2<-x1+0.02*sin60
>>  >  segments(x1,y2,x2,y1)
>>  >  text(x2+0.03,y1+0.015,as.character(rev(seq(10,90,by=10))))
>>  >  text(0.5,0.9,"100% clay")
>>  >  par(xpd=TRUE)
>>  >  text(-0.1,0,"100% sand")
>>  >  text(1.1,0,"100% loam")
>>  >  text(0.07,0.43,"percent clay")
>>  >  text(0.93,0.43,"percent silt")
>>  >  text(0.5,-0.1,"percent sand")
>>  >  # boundary of clay with extensions
>>  >  x1<-c(0.275,0.35,0.6)
>>  >  x2<-c(0.4,0.79,0.7)
>>  >  y1<-c(0.55*sin60,0.41*sin60,0.41*sin60)
>>  >  y2<-c(0.285*sin60,0.41*sin60,0.6*sin60)
>>  >  segments(x1,y1,x2,y2)
>>  >  text(0.5,0.57,"Clay")
>>  >  # lower bound of clay loam & silty divider
>>  >  x1<-c(0.4,0.68)
>>  >  x2<-c(0.86,0.6)
>>  >  y1<-c(0.285*sin60,0.285*sin60)
>>  >  y2<-c(0.285*sin60,0.41*sin60)
>>  >  segments(x1,y1,x2,y2)
>>  >  text(0.7,0.49*sin60,"Silty")
>>  >  text(0.7,0.44*sin60,"clay")
>>  >  text(0.73,0.37*sin60,"Silty clay")
>>  >  text(0.73,0.33*sin60,"loam")
>>  >  text(0.5,0.35*sin60,"Clay loam")
>>  >  x1<-c(0.185,0.1,0.37)
>>  >  x2<-c(0.36,0.37,0.4)
>>  >  y1<-c(0.37*sin60,0.2*sin60,0.2*sin60)
>>  >  y2<-c(0.37*sin60,0.2*sin60,0.285*sin60)
>>  >  segments(x1,y1,x2,y2)
>>  >  text(0.27,0.43*sin60,"Sandy")
>>  >  text(0.27,0.39*sin60,"clay")
>>  >  text(0.27,0.3*sin60,"Sandy clay")
>>  >  text(0.27,0.26*sin60,"loam")
>>  >  # sand corner
>>  >  x1<-c(0.05,0.075)
>>  >  x2<-c(0.12,0.3)
>>  >  y1<-c(0.1*sin60,0.15*sin60)
>>  >  y2<-c(0,0)
>>  >  segments(x1,y1,x2,y2)
>>  >  text(0.25,0.13*sin60,"Sandy loam")
>>  >  text(0.13,0.075*sin60,"Loamy")
>>  >  text(0.15,0.035*sin60,"sand")
>>  >  text(0.055,0.021,"Sand")
>>  >  x1<-c(0.37,0.42,0.5,0.8,0.86)
>>  >  x2<-c(0.42,0.54,0.65,0.86,0.94)
>>  >  y1<-c(0.2*sin60,0.08*sin60,0,0,0.12*sin60)
>>  >  y2<-c(0.08*sin60,0.08*sin60,0.285*sin60,0.12*sin60,0.12*sin60)
>>  >  segments(x1,y1,x2,y2)
>>  >  text(0.49,0.18*sin60,"Loam")
>>  >  text(0.72,0.15*sin60,"Silt loam")
>>  >  text(0.9,0.06*sin60,"Silt")
>>  >  par(oldpar)
>>  > }
>>
>> ______________________________________________
>> R-help@stat.math.ethz.ch mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide! 
>> http://www.R-project.org/posting-guide.html
>>

>
>
-- 
--------------------------------------------
Dr Sander P. Oom
Animal, Plant and Environmental Sciences,
University of the Witwatersrand
Private Bag 3, Wits 2050, South Africa
Tel (work)      +27 (0)11 717 64 04
Tel (home)      +27 (0)18 297 44 51
Fax             +27 (0)18 299 24 64
Email   sander@oomvanlieshout.net
Web     www.oomvanlieshout.net/sander

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Received on Sat May 28 06:32:22 2005

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