R help - Dec 2010 - colour-plot of point intensities?

Hi,

I've spent a while scrabbling around at this problem, to no avail. I'm
sure there /should/ be a simple answer...

I have a large (14 million rows) data set, with two columns. Each row
contains the number of times an individual moved, and the distance
that individual moved in total. I would like a figure where the colour
indicates the density of points, rather like this one my colleague
produced in Matlab (with an older version of the data):

http://www.warwick.ac.uk/~lssgah/warwick1.pdf

Sadly, my colleague is away at the moment, so I can't find out what
they did in Matlab. How should I be approaching this problem?
[ideally, I'd like a colour-scale like that, too, but]

My current approach, based on a bit in the back of Crawley's R book,
was to create a new data file where I rounded distance off, and
counted the number of similar rows to give a third column (a count). I
then did:

library(akima)
obs <- read.table("numvsdistscount.dat")
zz <- with(obs,interp(V1,V2,V3))
filled.contour(zz,col=heat.colors(12))

But:
i) I think doing a rounding step to create the third column (separate
from the plot generation) is unwise
ii) This results in a shaded area less than the full area of the plot
iii) The colour comes out almost uniform

I'd be grateful for any pointers.

Thanks,

Matthew

-- 
Matthew Vernon, Research Fellow
Ecology and Epidemiology Group,
University of Warwick
http://blogs.warwick.ac.uk/mcvernon

Look at the hexbin package (bioconductor).

-- 
Gregory (Greg) L. Snow Ph.D.
Statistical Data Center
Intermountain Healthcare
greg.snow at imail.org
801.408.8111

> -----Original Message-----
> From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-
> project.org] On Behalf Of Matthew Vernon
> Sent: Tuesday, December 14, 2010 9:48 AM
> To: r-help at stat.math.ethz.ch
> Subject: [R] colour-plot of point intensities?
> 
> Hi,
> 
> I've spent a while scrabbling around at this problem, to no avail.
I'm
> sure there /should/ be a simple answer...
> 
> I have a large (14 million rows) data set, with two columns. Each row
> contains the number of times an individual moved, and the distance
> that individual moved in total. I would like a figure where the colour
> indicates the density of points, rather like this one my colleague
> produced in Matlab (with an older version of the data):
> 
> http://www.warwick.ac.uk/~lssgah/warwick1.pdf
> 
> Sadly, my colleague is away at the moment, so I can't find out what
> they did in Matlab. How should I be approaching this problem?
> [ideally, I'd like a colour-scale like that, too, but]
> 
> My current approach, based on a bit in the back of Crawley's R book,
> was to create a new data file where I rounded distance off, and
> counted the number of similar rows to give a third column (a count). I
> then did:
> 
> library(akima)
> obs <- read.table("numvsdistscount.dat")
> zz <- with(obs,interp(V1,V2,V3))
> filled.contour(zz,col=heat.colors(12))
> 
> But:
> i) I think doing a rounding step to create the third column (separate
> from the plot generation) is unwise
> ii) This results in a shaded area less than the full area of the plot
> iii) The colour comes out almost uniform
> 
> I'd be grateful for any pointers.
> 
> Thanks,
> 
> Matthew
> 
> --
> Matthew Vernon, Research Fellow
> Ecology and Epidemiology Group,
> University of Warwick
> http://blogs.warwick.ac.uk/mcvernon
> 
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