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Pierre Bruyer

2011-May-23 09:55 UTC

[R] Get contour of a map

Hello everybody,

I search a function which returns the contour of map with levels like
contourLines, but I would like this function return the border of the map too,
because the function contourLines cannot consider the corner of the map and it
is not adapted to fill polygon after that.

Thanks in advance

Pierre Bruyer

Duncan Murdoch

2011-May-23 19:00 UTC

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[R] Get contour of a map

On 11-05-23 5:55 AM, Pierre Bruyer wrote:> Hello everybody,
>
> I search a function which returns the contour of map with levels like
contourLines, but I would like this function return the border of the map too,
because the function contourLines cannot consider the corner of the map and it
is not adapted to fill polygon after that.

I think writing that would be hard, but you can fake it.  Find the range 
of z first to work out the contour levels you want, then put very large 
values around the outside of the z matrix.  (You can't use Inf, but big 
finite values will work.)  For example:

x <- 1:10
y <- 1:20
z <- outer(x, y, function(x,y) sin(x)+cos(x*y/10))

range(z) # about -2 to 2, so 10000 is much bigger

z <- rbind(10000, z, 10000)
z <- cbind(10000, z, 10000)

x <- c(0.99, x, 10.01)
y <- c(0.99, y, 20.01)

Now contour plots of x,y,z with contour levels in the range of -2 to 2 
will show closed contours, and contourLines() will return paths around 
them.  They aren't exactly right (because 10000 is not infinity, and 
0.01 is not zero), but should be close enough for graphics purposes.

You'll have to write your own function to handle the general case, but 
it shouldn't be too hard.

Duncan Murdoch

David Winsemius

2011-May-24 08:52 UTC

head link

[R] Get contour of a map

On May 23, 2011, at 5:55 AM, Pierre Bruyer wrote:
> Hello everybody,
>
> I search a function which returns the contour of map with levels  
> like contourLines, but I would like this function return the border  
> of the map too, because the function contourLines cannot consider  
> the corner of the map and it is not adapted to fill polygon after  
> that.
Frank Harrell has a `perimeter` function in his `rms` package which he  
uses to establish (and optionally draw)  boundaries around 2D regions  
with sufficient data to yield meaningful estimates. The plotting is  
handed off to lattice functions. His default plotting function for 2D  
plotting is contourplot. It didn't take that long to make the  
transition to rms+lattice and I have been very pleased with the  
integration of the two.

There is also a chull  (convex hull) function although at the moment I  
do not remember which package it resides in.

>
> Thanks in advance
>
> Pierre Bruyer
> ______________________________________________
> 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, MD
West Hartford, CT

Pierre Bruyer

2011-May-24 12:48 UTC

head link

[R] Get contour of a map

Yes sure! I understand english very well but I am not very good when I wrote, so
I try to don't write too nonsense. I have post a precedent topic about that
but no one have find a response for the ensemble of the problem.

So, I would like to create a raster for a map in R. I have a dataset with
coordinates xy and for each points of a grid, and a z concentration in each
points. I would obtain the same result than the software "Surfer 9". I
have two constraints:

- a scale of colors for the rasters (and the colors).
- for aesthetic, the contours of each scale must be smooth

Now an exemple with imaginary data (My datasets have 10000 points):

x =
c(0,0.1,0.2,0.3,0.4,0.5,0.6,0.7,0.8,0.9,1.0,0,0.1,0.2,0.3,0.4,0.5,0.6,0.7,0.8,0.9,1.0,0,0.1,0.2,0.3,0.4,0.5,0.6,0.7,0.8,0.9,1.0,0,0.1,0.2,0.3,0.4,0.5,0.6,0.7,0.8,0.9,1.0,0,0.1,0.2,0.3,0.4,0.5,0.6,0.7,0.8,0.9,1.0,0,0.1,0.2,0.3,0.4,0.5,0.6,0.7,0.8,0.9,1.0,0,0.1,0.2,0.3,0.4,0.5,0.6,0.7,0.8,0.9,1.0,0,0.1,0.2,0.3,0.4,0.5,0.6,0.7,0.8,0.9,1.0,0,0.1,0.2,0.3,0.4,0.5,0.6,0.7,0.8,0.9,1.0,0,0.1,0.2,0.3,0.4,0.5,0.6,0.7,0.8,0.9,1.0,0,0.1,0.2,0.3,0.4,0.5,0.6,0.7,0.8,0.9,1.0)
y =
c(0,0,0,0,0,0,0,0,0,0,0,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.2,0.2,0.2,0.2,0.2,0.2,0.2,0.2,0.2,0.2,0.2,0.3,0.3,0.3,0.3,0.3,0.3,0.3,0.3,0.3,0.3,0.3,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.4,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.7,0.7,0.7,0.7,0.7,0.7,0.7,0.7,0.7,0.7,0.7,0.8,0.8,0.8,0.8,0.8,0.8,0.8,0.8,0.8,0.8,0.8,0.9,0.9,0.9,0.9,0.9,0.9,0.9,0.9,0.9,0.9,0.9,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0)
z =
c(0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,10,5,6,0,0,0,0,0,0,0,0,0,3,6,9,15,14,12,0,0,0,0,0,0,0,0,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0)

essai <- data.frame(x =x, y = y, z = z)

level3 <- matrix(0,6,4)

level3[1,1] <- 1
level3[2,1] <- 5
level3[3,1] <- 10
level3[4,1] <- 15
level3[5,1] <- 25
level3[6,1] <- 30

level3[1,2] <- 0
level3[2,2] <- 0
level3[3,2] <- 0
level3[4,2] <- 0
level3[5,2] <- 255
level3[6,2] <- 255

level3[1,3] <- 0
level3[2,3] <- 0
level3[3,3] <- 255
level3[4,3] <- 255
level3[5,3] <- 0
level3[6,3] <- 0

level3[1,4] <- 0
level3[2,4] <- 255
level3[3,4] <- 0
level3[4,4] <- 255
level3[5,4] <- 0
level3[6,4] <- 255


## grd is the xyz dataframe, level is the matrix level3,and map_output is the
path where
##you want save the image.
create_map <- function(grd, level ,map_output, format = c("jpeg"),
width_map = 150, height_map = 150,...)
{

	grd2 <- matrix(grd[,3], nrow = sqrt(length(grd[,3])), ncol =
sqrt(length(grd[,3])), byrow = 		FALSE)

	##creation of breaks for colors
	i<-1	
	paliers <- c(-1.0E300)
	while(i<=length(level[,1]))
	{
		paliers <- c(paliers,level[i,1])
		i <- i+1
	}
	paliers <- c(paliers, 1.0E300)

	##scale color creation
	i <- 1
	colgraph <- c(rgb(255,255,255, maxColorValue = 255))
	while(i<=length(level[,2]))
	{
		colgraph <- c(colgraph, rgb(level[i,2],level[i,3],level[i,4], maxColorValue
= 255))
		i <- i +1
	}

### now many possibilities, this is the possibility with get contour of map
	
	grd2 <- rbind(-1E100, grd2, -1E100)	
	grd2 <- cbind(-1E100, grd2, -1E100)

	x <- seq(from=min(grd[,1]), to=max(grd[,1]), length = sqrt(length(grd[,1])))
	y <- seq(from=min(grd[,2]), to=max(grd[,2]), length = sqrt(length(grd[,2])))
	
	x <- c(min(grd[,1])-0.01, x , max(grd[,1])+0.01)
	y <- c(min(grd[,2])-0.01, y , max(grd[,2])+0.01)

	contours <- contourLines(x, y,grd2,levels=paliers)

	
	##user can choose the output format (default is jpeg)
	switch(format,  
		png = png(map_output, width = width_map, height = height_map) ,
		jpeg = jpeg(map_output, width = width_map, height = height_map, quality =
100),
		bmp = bmp(map_output, width = width_map, height = height_map),
		tiff = tiff(map_output, width = width_map, height = height_map),
		jpeg(map_output, width = width_map, height = height_map))


	## drawing map
		par(mar=c(0,0,0,0),xaxs="i", yaxs="i")

	plot(0,col="white",main="polygon()", asp = 1, axes = FALSE,
ann = FALSE,xlim=c(min(grd[,1	]),max(grd[,1])), ylim =
c(min(grd[,2]),max(grd[,2])),type = "n")

	for (i in seq_along(contours)) {
		 x <- contours[[i]]$x
		 y <- contours[[i]]$y
		 c <- contours[[i]]$level
		 j <- 1
		 tmp <- 0 
		 while(j < length(level[,1])+1 && tmp == 0){
			if( c == paliers[j]){
		 		tmp <- j
		 	}
		 	j <- j+1 
		}	
		a <- spline( seq_along(x), x)$y
		b <- spline( seq_along(y), y)$y
		polygon( a, b ,col = colgraph[tmp], border = NA)
	}
	
	dev.off() 		
}

Here I use the solution of Duncan Murdoch, it is almost that I want, now I try
to resolve the default of his methods, e.g. I don't want smooth the contour
( the border) of my raster.

Thank for your help :-))
(Sorry for the spam, I have forgotten to send the mail to r-help)

Le 24 mai 2011 ? 12:23, David Winsemius a ?crit :
> 
> On May 24, 2011, at 5:40 AM, Pierre Bruyer wrote:
> 
>> I have seen this package and especially the 'perimeter'
function, and it has not a 'levels' parameters like a lot of other
functions, and this is a big problem for my project.
> 
> Without a reproducible example it is difficult to know what you expect from
a `levels` parameter, but I can get particular contour levels to be drawn for
crossed-cubic regression splines. It would be more productive if you offered a
minimal example to be worked on.
> 
> -- 
> David.
>> Otherwise I find this package have a better architecture than the other
spatial package ^^
>> 
>> 
>> Le 24 mai 2011 ? 10:52, David Winsemius a ?crit :
>> 
>>> 
>>> On May 23, 2011, at 5:55 AM, Pierre Bruyer wrote:
>>> 
>>>> Hello everybody,
>>>> 
>>>> I search a function which returns the contour of map with
levels like contourLines, but I would like this function return the border of
the map too, because the function contourLines cannot consider the corner of the
map and it is not adapted to fill polygon after that.
>>> 
>>> Frank Harrell has a `perimeter` function in his `rms` package which
he uses to establish (and optionally draw)  boundaries around 2D regions with
sufficient data to yield meaningful estimates. The plotting is handed off to
lattice functions. His default plotting function for 2D plotting is contourplot.
It didn't take that long to make the transition to rms+lattice and I have
been very pleased with the integration of the two.
>>> 
>>> There is also a chull  (convex hull) function although at the
moment I do not remember which package it resides in.
>>> 
>>> 
>>>> 
>>>> Thanks in advance
>>>> 
>>>> Pierre Bruyer
>>>> ______________________________________________
>>>> 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, MD
>>> West Hartford, CT
>>> 
>> 
> 
> David Winsemius, MD
> West Hartford, CT
>

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