[BioC] pairs() with hexbin panels (was RE: hexbin needs colorspac e - but where is colorspace?)
andy_liaw at merck.com
Tue Jul 19 16:30:34 CEST 2005
I recently ran into related problems. I was looking for a way to do pairs()
with hexbin in each panel. I found pairs.CSP() in `rflowcyt', but even the
example code in ?pairs.CSP failed. (That example code is wrapped in `if
(interactive()) ...', so R CMD check would not have picked it up.) The
culprit is that hexagons() is no where to be found. I suspect this is
caused by hexbin version incompatibility?
Can anyone suggest a way to do what I want (scatterplot matrix with hexbin
> From: Martin Maechler
> >>>>> "JimMcD" == James MacDonald <jmacdon at med.umich.edu>
> >>>>> on Mon, 18 Jul 2005 15:23:19 -0400 writes:
> JimMcD> library(reposTools)
> JimMcD> install.packages2("colorspace")
> JimMcD> HTH,
> JimMcD> Jim
> JimMcD> Also, if you are using the devel version you will
> probably need to be
> JimMcD> running R-2.2.0
> but really the grid-based hexbin is in the current Bioconductor
> (1.6), at least for me,
> so I am a little perplexed why Naomi first needs to download it.
> I guess, Naomi, you somehow managed to keep an old version of
> hexbin around? It may be because getBioC() has changed and
> doesn't install "hexbin" anymore AFAIK, unless you explicitly
> ask for
> getBioC("hexbin", lib = ...., destdir = ....)
> the need of which I had been wondering about as well..
> Also --- probably more a question to the
> bioconductor-release-managers :
> if you had used the above getBioC(..) shouldn't you have gotten
> "hexbin" *plus* all the packages it depends on, i.e., in your
> case "colorspace" as well?
> Naomi, can you tell us *how* you've installed hexbin?
> Martin Maechler, ETH Zurich
> >>>> Naomi Altman <naomi at stat.psu.edu> 7/18/2005 3:15:30 PM >>>
> Naomi> I downloaded hexbin from the developer site, since
> the release version
> Naomi> says
> Naomi> to do so.
> Naomi> But I then get the following message:
> >> library(hexbin)
> Naomi> Loading required package: grid
> Naomi> Loading required package: colorspace
> Naomi> Error: package 'colorspace' could not be loaded
> Naomi> In addition: Warning message:
> Naomi> there is no package called 'colorspace' in:
> library(pkg, character.only
> Naomi> = TRUE, logical = TRUE, lib.loc = lib.loc)
> Naomi> I thought this might be a version problem, so I also
> Naomi> reinstalled the most recent version of R - but to no
> Naomi> avail. I have not been able to locate colorspace.
> Naomi> As always, any assistance would be most appreciated.
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