How can I recreate this 2d surface + contour + glyph plot in R? - r

Question

I've run a 2d simulation in some modelling software from which i've got an export of x,y point locations with a set of 6 attributes. I wish to recreate a figure that combines the data, like this:
The ellipses and the background are shaded according to attribute 1 (and the borders of these are of course representing the model geometry, but I don't think I can replicate that), the isolines are contours of attribute 2, and the arrow glyphs are from attributes 3 (x magnitude) and 4 (y magnitude).
The x,y points are centres of the triangulated mesh I think, and look like this:
I want to know how I can recreate a plot like this with R. To start with I have irregularly-spaced data due to it being exported from an irregular mesh. That's immediately where I get stuck with R, having only ever used it for producing box-and-whisper plots and the like.
Here's the data:
https://dl.dropbox.com/u/22417033/Ellipses_noheader.txt
Edit: fields: x, y, heat flux (x), heat flux (y), thermal conductivity, Temperature, gradT (x), gradT (y).
names(Ellipses) <- c('x','y','dfluxx','dfluxy','kxx','Temps','gradTx','gradTy')

Answer 1

It's quite easy to make the lower plot (making the assumption that there is a dataframe named 'edat' read in with:
edat <- read.table(file=file.choose())
with(edat, plot(V1,V2), cex=0.2)
Things get a bit more beautiful with:
with(edat, plot(V1,V2, cex=0.2, col=V5))
So I do not think your original is being faithfully represented by the data. The contour lines are NOT straight across the "conductors". I call them "conductors" because this looks somewhat like iso-potential lines in electrostatics. I'm adding some text here to serve as a search handle for others who might be searching for plotting problems in real world physics: vector-field (the arrows) , heat equations, gradient, potential lines.
You can then overlay the vector field with:
with(edat, arrows(V1,V2, V1-20*V6*V7, V2-20*V6*V8, length=0.04, col="orange") )
You could"zoom in" with xlim and ylim:
with(edat, plot(V1,V2, cex=0.3, col=V5, xlim=c(0, 10000), ylim=c(-8000, -2000) ))
with(edat, arrows(V1,V2, V1-20*V6*V7, V2-20*V6*V8, length=0.04, col="orange") )
Guessing that the contour requested if for the Temps variable. Take your pick of contourplots.
require(akima)
intflow<- with(edat, interp(x=x, y=y, z=Temps, xo=seq(min(x), max(x), length = 410),
yo=seq(min(y), max(y), length = 410), duplicate="mean", linear=FALSE) )
require(lattice)
contourplot(intflow$z)
filled.contour(intflow)
with( intflow, contour(x=x, y=y, z=z) )
The last one will mix with the other plotting examples since those were using base plotting functions. You may need to switch to points instead of plot.

Answer 2

There are several parts to your plot so you will probably need several tools to make the different parts.
The background and ellipses can be created with polygon (once you figure where they should be).
The contourLines function can calculate the contour lines for you which you can add with the lines function (or contour has and add argument and could probably be used to add the lines directly).
The akima package has a function interp which can estimate values on a grid given the values ungridded.
The my.symbols function along with ms.arrows, both from the TeachingDemos package, can be used to draw the vector field.

Answer 3

#DWin is right to say that your graph don't represent faithfully your data, so I would advice to follow his answer. However here is how to reproduce (the closest I could) your graph:
Ellipses <- read.table(file.choose())
names(Ellipses) <- c('x','y','dfluxx','dfluxy','kxx','Temps','gradTx','gradTy')
require(splancs)
require(akima)
First preparing the data:
#First the background layer (the 'kxx' layer):
# Here the regular grid on which we're gonna do the interpolation
E.grid <- with(Ellipses,
expand.grid(seq(min(x),max(x),length=200),
seq(min(y),max(y),length=200)))
names(E.grid) <- c("x","y") # Without this step, function inout throws an error
E.grid$Value <- rep(0,nrow(E.grid))
#Split the dataset according to unique values of kxx
E.k <- split(Ellipses,Ellipses$kxx)
# Find the convex hull delimiting each of those values domain
E.k.ch <- lapply(E.k,function(X){X[chull(X$x,X$y),]})
for(i in unique(Ellipses$kxx)){ # Pick the value for each coordinate in our regular grid
E.grid$Value[inout(E.grid[,1:2],E.k.ch[names(E.k.ch)==i][[1]],bound=TRUE)]<-i
}
# Then the regular grid for the second layer (Temp)
T.grid <- with(Ellipses,
interp(x,y,Temps, xo=seq(min(x),max(x),length=200),
yo=seq(min(y),max(y),length=200),
duplicate="mean", linear=FALSE))
# The regular grids for the arrow layer (gradT)
dx <- with(Ellipses,
interp(x,y,gradTx,xo=seq(min(x),max(x),length=15),
yo=seq(min(y),max(y),length=10),
duplicate="mean", linear=FALSE))
dy <- with(Ellipses,
interp(x,y,gradTy,xo=seq(min(x),max(x),length=15),
yo=seq(min(y),max(y),length=10),
duplicate="mean", linear=FALSE))
T.grid2 <- with(Ellipses,
interp(x,y,Temps, xo=seq(min(x),max(x),length=15),
yo=seq(min(y),max(y),length=10),
duplicate="mean", linear=FALSE))
gradTgrid<-expand.grid(dx$x,dx$y)
And then the plotting:
palette(grey(seq(0.5,0.9,length=5)))
par(mar=rep(0,4))
plot(E.grid$x, E.grid$y, col=E.grid$Value,
axes=F, xaxs="i", yaxs="i", pch=19)
contour(T.grid, add=TRUE, col=colorRampPalette(c("blue","red"))(15), drawlabels=FALSE)
arrows(gradTgrid[,1], gradTgrid[,2], # Here I multiply the values so you can see them
gradTgrid[,1]-dx$z*40*T.grid2$z, gradTgrid[,2]-dy$z*40*T.grid2$z,
col="yellow", length=0.05)
To understand in details how this code works, I advise you to read the following help pages: ?inout, ?chull, ?interp, ?expand.grid and ?contour.