Message: 6 Date: Tue, 19 Jul 2005 10:30:34 -0400 From: "Liaw, Andy" <andy_liaw@merck.com> Hi, Been off the list a while so I am late replying to this. Colorspace: The colorspace package is needed by the current version of hexbin, but I will be changing that very soon as all the color functionality I needed is now in graphics. Specifically I need it for hexdiff plots with multiple groups to do color intersections. pairs Plots: I am working on functions and classes to do this. The big problem is a layout function that will set up the aspect ratios properly on the page. I have written some functions for lattice that do hexagon binning for the panel functions on the fly, but it needs some tweeking. Nicholas Subject: [BioC] pairs() with hexbin panels (was RE: hexbin needs colorspac e - but where is colorspace?) To: "'Martin Maechler'" <maechler at="" stat.math.ethz.ch="">, "James MacDonald" <jmacdon at="" med.umich.edu=""> Cc: naomi at stat.psu.edu, bioconductor at stat.math.ethz.ch Message-ID: <39B6DDB9048D0F4DAD42CB26AAFF0AFA64EAC9 at usctmx1106.Merck.com> Content-Type: text/plain 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 panels)? Best, Andy > 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? > > Regards, > 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. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > > >