Re: [R] Puzzled with contour()

From: Gabor Grothendieck <ggrothendieck_at_gmail.com>
Date: Tue 27 Jun 2006 - 22:40:56 EST

On 6/27/06, Martin Maechler <maechler@stat.math.ethz.ch> wrote:
> >>>>> "Gabor" == Gabor Grothendieck <ggrothendieck@gmail.com>
> >>>>> on Mon, 26 Jun 2006 11:28:48 -0400 writes:
>
> Gabor> I think its often the case that one has 3 tuples and does not know
> Gabor> how to use contour with that; so, it would be nice if the contour
> Gabor> help page gave advice and an example and a pointer to the relevant
> Gabor> functions if it cannot be done by contour.
>
> Yes, but even more importantly,
> what help(contour) should really have is a \code{\link[lattice]{contourplot}}
> since contourplot() from package 'lattice'
> can deal well excellently with the situation Ajay has:
>
> After reading his data into matrix 'm3'
>
> > d3 <- data.frame(m3)
> > summary(d3)
> x y z
> Min. :0.00 Min. : 20 Min. :0.0000
> 1st Qu.:0.25 1st Qu.: 60 1st Qu.:0.0000
> Median :0.50 Median :110 Median :0.0040
> Mean :0.50 Mean :110 Mean :0.1583
> 3rd Qu.:0.75 3rd Qu.:160 3rd Qu.:0.1410
> Max. :1.00 Max. :200 Max. :1.0000
>
> contourplot(z ~ x+y, data=d3)
> ## or nicer
> contourplot(z ~ x+y, data=d3, cuts=20, region = TRUE)
> ## or rather use logit - transformed z values:
> contourplot(qlogis(z) ~ x+y, data=d3, cuts=20, region = TRUE)
>
> Gabor> On 6/26/06, Duncan Murdoch <murdoch@stats.uwo.ca> wrote:
> >> On 6/26/2006 10:39 AM, Gabor Grothendieck wrote:
> >> > I think it would be helpful if this were added to the contour help file.
> >>
> >> You mean an example of building up the z matrix from points, or just a
> >> general discussion of the issue?
> >>
> >> Duncan Murdoch
> >> >
> >> > On 6/26/06, Duncan Murdoch <murdoch@stats.uwo.ca> wrote:
> >> >> On 6/25/2006 9:33 AM, Ajay Narottam Shah wrote:
> >> >> > Folks,
> >> >> >
> >> >> > The contour() function wants x and y to be in increasing order. I have
> >> >> > a situation where I have a grid in x and y, and associated z values,
> >> >> > which looks like this:
> >> >>
> >> >> contour() wants vectors of x and y values, and a matrix of z values,
> >> >> where the x values correspond to the rows of z, and the y values to the
> >> >> columns. You have a collection of points which need to be turned into
> >> >> such a grid.
> >> >>
> >> >> There's an interp function in the akima package that can do this in
> >> >> general. In your case, it's probably sufficient to do something like this:
> >> >>
> >> >> zmat <- matrix(NA, 3, 19)
> >> >> zmat[cbind(20*x + 1, y/10 - 1)] <- z
> >> >> x <- (0:2)/20
> >> >> y <- (2:20)*10
> >> >> contour(x,y,zmat)
> >> >>
> >> >> Duncan Murdoch
> >> >>
> >> >>
> >> >> >
> >> >> > x y z
> >> >> > [1,] 0.00 20 1.000
> >> >> > [2,] 0.00 30 1.000
> >> >> > [3,] 0.00 40 1.000
> >> >> > [4,] 0.00 50 1.000
> >> >> > [5,] 0.00 60 1.000
> >> >> > [6,] 0.00 70 1.000
> >> >> > [7,] 0.00 80 0.000
> >> >> > [8,] 0.00 90 0.000
> >> >> > [9,] 0.00 100 0.000
> >> >> > [10,] 0.00 110 0.000
> >> >> > [11,] 0.00 120 0.000
> >> >> > [12,] 0.00 130 0.000
> >> >> > [13,] 0.00 140 0.000
> >> >> > [14,] 0.00 150 0.000
> >> >> > [15,] 0.00 160 0.000
> >> >> > [16,] 0.00 170 0.000
> >> >> > [17,] 0.00 180 0.000
> >> >> > [18,] 0.00 190 0.000
> >> >> > [19,] 0.00 200 0.000
> >> >> > [20,] 0.05 20 1.000
> >> >> > [21,] 0.05 30 1.000
> >> >> > [22,] 0.05 40 1.000
> >> >> > [23,] 0.05 50 1.000
> >> >> > [24,] 0.05 60 0.998
> >> >> > [25,] 0.05 70 0.124
> >> >> > [26,] 0.05 80 0.000
> >> >> > [27,] 0.05 90 0.000
> >> >> > [28,] 0.05 100 0.000
> >> >> > [29,] 0.05 110 0.000
> >> >> > [30,] 0.05 120 0.000
> >> >> > [31,] 0.05 130 0.000
> >> >> > [32,] 0.05 140 0.000
> >> >> > [33,] 0.05 150 0.000
> >> >> > [34,] 0.05 160 0.000
> >> >> > [35,] 0.05 170 0.000
> >> >> > [36,] 0.05 180 0.000
> >> >> > [37,] 0.05 190 0.000
> >> >> > [38,] 0.05 200 0.000
> >> >> > [39,] 0.10 20 1.000
> >> >> > [40,] 0.10 30 1.000
> >> >> >
> >> >> > This looks like a nice case where both x and y are in increasing
> >> >> > order. But contour() gets unhappy saying that he wants x and y in
> >> >> > increasing order.
> >> >> >
> >> >> > Gnuplot generates pretty 3d pictures from such data, where you are
> >> >> > standing above a surface and looking down at it. How does one do that
> >> >> > in R?
> >> >> >
> >> >> > Any help will be most appreciated. A dput() of my data object is :
> >> >> >
> >> >> > structure(c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
> >> >> > 0, 0, 0.05, 0.05, 0.05, 0.05, 0.05, 0.05, 0.05, 0.05, 0.05, 0.05,
> >> >> > 0.05, 0.05, 0.05, 0.05, 0.05, 0.05, 0.05, 0.05, 0.05, 0.1, 0.1,
> >> >> > 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1,
> >> >> > 0.1, 0.1, 0.1, 0.1, 0.15, 0.15, 0.15, 0.15, 0.15, 0.15, 0.15,
> >> >> > 0.15, 0.15, 0.15, 0.15, 0.15, 0.15, 0.15, 0.15, 0.15, 0.15, 0.15,
> >> >> > 0.15, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2,
> >> >> > 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.25, 0.25, 0.25, 0.25,
> >> >> > 0.25, 0.25, 0.25, 0.25, 0.25, 0.25, 0.25, 0.25, 0.25, 0.25, 0.25,
> >> >> > 0.25, 0.25, 0.25, 0.25, 0.3, 0.3, 0.3, 0.3, 0.3, 0.3, 0.3, 0.3,
> >> >> > 0.3, 0.3, 0.3, 0.3, 0.3, 0.3, 0.3, 0.3, 0.3, 0.3, 0.3, 0.35,
> >> >> > 0.35, 0.35, 0.35, 0.35, 0.35, 0.35, 0.35, 0.35, 0.35, 0.35, 0.35,
> >> >> > 0.35, 0.35, 0.35, 0.35, 0.35, 0.35, 0.35, 0.4, 0.4, 0.4, 0.4,
> >> >> > 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4,
> >> >> > 0.4, 0.4, 0.45, 0.45, 0.45, 0.45, 0.45, 0.45, 0.45, 0.45, 0.45,
> >> >> > 0.45, 0.45, 0.45, 0.45, 0.45, 0.45, 0.45, 0.45, 0.45, 0.45, 0.5,
> >> >> > 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5,
> >> >> > 0.5, 0.5, 0.5, 0.5, 0.5, 0.55, 0.55, 0.55, 0.55, 0.55, 0.55,
> >> >> > 0.55, 0.55, 0.55, 0.55, 0.55, 0.55, 0.55, 0.55, 0.55, 0.55, 0.55,
> >> >> > 0.55, 0.55, 0.6, 0.6, 0.6, 0.6, 0.6, 0.6, 0.6, 0.6, 0.6, 0.6,
> >> >> > 0.6, 0.6, 0.6, 0.6, 0.6, 0.6, 0.6, 0.6, 0.6, 0.65, 0.65, 0.65,
> >> >> > 0.65, 0.65, 0.65, 0.65, 0.65, 0.65, 0.65, 0.65, 0.65, 0.65, 0.65,
> >> >> > 0.65, 0.65, 0.65, 0.65, 0.65, 0.7, 0.7, 0.7, 0.7, 0.7, 0.7, 0.7,
> >> >> > 0.7, 0.7, 0.7, 0.7, 0.7, 0.7, 0.7, 0.7, 0.7, 0.7, 0.7, 0.7, 0.75,
> >> >> > 0.75, 0.75, 0.75, 0.75, 0.75, 0.75, 0.75, 0.75, 0.75, 0.75, 0.75,
> >> >> > 0.75, 0.75, 0.75, 0.75, 0.75, 0.75, 0.75, 0.8, 0.8, 0.8, 0.8,
> >> >> > 0.8, 0.8, 0.8, 0.8, 0.8, 0.8, 0.8, 0.8, 0.8, 0.8, 0.8, 0.8, 0.8,
> >> >> > 0.8, 0.8, 0.85, 0.85, 0.85, 0.85, 0.85, 0.85, 0.85, 0.85, 0.85,
> >> >> > 0.85, 0.85, 0.85, 0.85, 0.85, 0.85, 0.85, 0.85, 0.85, 0.85, 0.9,
> >> >> > 0.9, 0.9, 0.9, 0.9, 0.9, 0.9, 0.9, 0.9, 0.9, 0.9, 0.9, 0.9, 0.9,
> >> >> > 0.9, 0.9, 0.9, 0.9, 0.9, 0.95, 0.95, 0.95, 0.95, 0.95, 0.95,
> >> >> > 0.95, 0.95, 0.95, 0.95, 0.95, 0.95, 0.95, 0.95, 0.95, 0.95, 0.95,
> >> >> > 0.95, 0.95, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
> >> >> > 1, 1, 20, 30, 40, 50, 60, 70, 80, 90, 100, 110, 120, 130, 140,
> >> >> > 150, 160, 170, 180, 190, 200, 20, 30, 40, 50, 60, 70, 80, 90,
> >> >> > 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, 200, 20, 30,
> >> >> > 40, 50, 60, 70, 80, 90, 100, 110, 120, 130, 140, 150, 160, 170,
> >> >> > 180, 190, 200, 20, 30, 40, 50, 60, 70, 80, 90, 100, 110, 120,
> >> >> > 130, 140, 150, 160, 170, 180, 190, 200, 20, 30, 40, 50, 60, 70,
> >> >> > 80, 90, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, 200,
> >> >> > 20, 30, 40, 50, 60, 70, 80, 90, 100, 110, 120, 130, 140, 150,
> >> >> > 160, 170, 180, 190, 200, 20, 30, 40, 50, 60, 70, 80, 90, 100,
> >> >> > 110, 120, 130, 140, 150, 160, 170, 180, 190, 200, 20, 30, 40,
> >> >> > 50, 60, 70, 80, 90, 100, 110, 120, 130, 140, 150, 160, 170, 180,
> >> >> > 190, 200, 20, 30, 40, 50, 60, 70, 80, 90, 100, 110, 120, 130,
> >> >> > 140, 150, 160, 170, 180, 190, 200, 20, 30, 40, 50, 60, 70, 80,
> >> >> > 90, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, 200, 20,
> >> >> > 30, 40, 50, 60, 70, 80, 90, 100, 110, 120, 130, 140, 150, 160,
> >> >> > 170, 180, 190, 200, 20, 30, 40, 50, 60, 70, 80, 90, 100, 110,
> >> >> > 120, 130, 140, 150, 160, 170, 180, 190, 200, 20, 30, 40, 50,
> >> >> > 60, 70, 80, 90, 100, 110, 120, 130, 140, 150, 160, 170, 180,
> >> >> > 190, 200, 20, 30, 40, 50, 60, 70, 80, 90, 100, 110, 120, 130,
> >> >> > 140, 150, 160, 170, 180, 190, 200, 20, 30, 40, 50, 60, 70, 80,
> >> >> > 90, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, 200, 20,
> >> >> > 30, 40, 50, 60, 70, 80, 90, 100, 110, 120, 130, 140, 150, 160,
> >> >> > 170, 180, 190, 200, 20, 30, 40, 50, 60, 70, 80, 90, 100, 110,
> >> >> > 120, 130, 140, 150, 160, 170, 180, 190, 200, 20, 30, 40, 50,
> >> >> > 60, 70, 80, 90, 100, 110, 120, 130, 140, 150, 160, 170, 180,
> >> >> > 190, 200, 20, 30, 40, 50, 60, 70, 80, 90, 100, 110, 120, 130,
> >> >> > 140, 150, 160, 170, 180, 190, 200, 20, 30, 40, 50, 60, 70, 80,
> >> >> > 90, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, 200, 20,
> >> >> > 30, 40, 50, 60, 70, 80, 90, 100, 110, 120, 130, 140, 150, 160,
> >> >> > 170, 180, 190, 200, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0,
> >> >> > 0, 0, 0, 0, 0, 1, 1, 1, 1, 0.998, 0.124, 0, 0, 0, 0, 0, 0, 0,
> >> >> > 0, 0, 0, 0, 0, 0, 1, 1, 1, 0.998, 0.71, 0.068, 0, 0, 0, 0, 0,
> >> >> > 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 0.998, 0.898, 0.396, 0.058, 0.002,
> >> >> > 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0.998, 0.97, 0.726, 0.268,
> >> >> > 0.056, 0.006, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0.996, 0.88,
> >> >> > 0.546, 0.208, 0.054, 0.012, 0.002, 0, 0, 0, 0, 0, 0, 0, 0, 0,
> >> >> > 0, 0, 0.998, 0.964, 0.776, 0.418, 0.18, 0.054, 0.014, 0.002,
> >> >> > 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.998, 0.906, 0.664, 0.342,
> >> >> > 0.166, 0.056, 0.018, 0.006, 0.002, 0, 0, 0, 0, 0, 0, 0, 0, 0,
> >> >> > 0, 0.986, 0.862, 0.568, 0.29, 0.15, 0.056, 0.022, 0.008, 0.002,
> >> >> > 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.954, 0.778, 0.494, 0.26, 0.148,
> >> >> > 0.056, 0.024, 0.012, 0.004, 0.002, 0, 0, 0, 0, 0, 0, 0, 0, 0,
> >> >> > 0.906, 0.712, 0.43, 0.242, 0.144, 0.058, 0.028, 0.012, 0.006,
> >> >> > 0.002, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.878, 0.642, 0.38, 0.222,
> >> >> > 0.142, 0.066, 0.034, 0.014, 0.008, 0.004, 0.002, 0, 0, 0, 0,
> >> >> > 0, 0, 0, 0, 0.846, 0.586, 0.348, 0.208, 0.136, 0.068, 0.034,
> >> >> > 0.016, 0.012, 0.006, 0.004, 0.002, 0, 0, 0, 0, 0, 0, 0, 0.8,
> >> >> > 0.538, 0.318, 0.204, 0.136, 0.07, 0.046, 0.024, 0.012, 0.008,
> >> >> > 0.004, 0.002, 0.002, 0, 0, 0, 0, 0, 0, 0.762, 0.496, 0.294, 0.2,
> >> >> > 0.138, 0.072, 0.05, 0.024, 0.014, 0.012, 0.006, 0.004, 0.002,
> >> >> > 0.002, 0, 0, 0, 0, 0, 0.704, 0.472, 0.286, 0.198, 0.138, 0.074,
> >> >> > 0.054, 0.028, 0.016, 0.012, 0.008, 0.006, 0.004, 0.002, 0.002,
> >> >> > 0, 0, 0, 0, 0.668, 0.438, 0.276, 0.196, 0.138, 0.078, 0.054,
> >> >> > 0.032, 0.024, 0.014, 0.012, 0.008, 0.004, 0.004, 0.002, 0.002,
> >> >> > 0, 0, 0, 0.634, 0.412, 0.27, 0.194, 0.14, 0.086, 0.056, 0.032,
> >> >> > 0.024, 0.016, 0.012, 0.01, 0.006, 0.004, 0.004, 0.002, 0.002,
> >> >> > 0, 0, 0.604, 0.388, 0.26, 0.19, 0.144, 0.088, 0.058, 0.048, 0.026,
> >> >> > 0.022, 0.014, 0.012, 0.008, 0.006, 0.004, 0.004, 0.002, 0.002,
> >> >> > 0, 0.586, 0.376, 0.256, 0.19, 0.146, 0.094, 0.062, 0.052, 0.028,
> >> >> > 0.024, 0.014, 0.012, 0.012, 0.008, 0.004, 0.004, 0.004, 0.002,
> >> >> > 0.002, 0.566, 0.364, 0.254, 0.192, 0.148, 0.098, 0.064, 0.054,
> >> >> > 0.032, 0.024, 0.022, 0.014, 0.012, 0.012, 0.008, 0.004, 0.004,
> >> >> > 0.004, 0.002), .Dim = c(399, 3), .Dimnames = list(NULL, c("x",
> >> >> > "y", "z")))
> >> >> >
> >> >> > --
> >> >> > Ajay Shah http://www.mayin.org/ajayshah
> >> >> > ajayshah_at_mayin.org http://ajayshahblog.blogspot.com
> >> >> > <*(:-? - wizard who doesn't know the answer.
> >> >> >
> >> >> > ______________________________________________
> >> >> > 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
> >> >>
> >> >> ______________________________________________
> >> >> 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
> >> >>
> >> >
> >> > ______________________________________________
> >> > 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
> >>
> >>
>
> Gabor> ______________________________________________
> Gabor> R-help@stat.math.ethz.ch mailing list
> Gabor> https://stat.ethz.ch/mailman/listinfo/r-help
> Gabor> PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
>

Or perhaps contour should be extended so that it can handle triples giving the capability directly in base graphics. I think that that is what many people really expect.



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 Received on Tue Jun 27 22:57:07 2006

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