On 7/14/07, Stephen Tucker <[EMAIL PROTECTED]> wrote: > > I wonder what kind of objects? Are there large advantages for allowing > lattice functions to operate on objects other than data frames - I > couldn't find any screenshots of flowViz but I imagine those objects > would probably be list of arrays and such? I tend to think of mapply() > [and more recently melt()], etc. could always be applied beforehand, > but I suppose that would undermine the case for having generic > functions to support the rich collection of object classes in R...
There's a copy of a presentation at http://www.ficcs.org/meetings/ficcs3/presentations/DeepayanSarkar-flowviz.pdf and a (largish - 37M) vignette linked from http://bioconductor.org/packages/2.1/bioc/html/flowViz.html Neither of these really talk about the challenge posed by the size of the data. The data structure, as with most microarray-type experiments, is like a data frame, except that the response for every experimental unit is itself a large matrix. If we represented the GvHD data set (the one used in the examples) as a "long format" data frame that lattice would understand, it would have 585644 rows and 12 columns (8 measurements that are different for each row, and 4 phenotypic variables that are the same for all rows coming from a single sample). And this is for a smallish subset of the actual experiment. In practice, the data are stored in an environment to prevent unnecessary copying, and panel functions only access one data matrix at a time. -Deepayan > --- Deepayan Sarkar <[EMAIL PROTECTED]> wrote: > > > On 7/11/07, hadley wickham <[EMAIL PROTECTED]> wrote: > > > > A question/comment: I have usually found that the subscripts argument > > is > > > > what I need when passing *external* information into the panel > > function, for > > > > example, when I wish to add results from a fit done external to the > > trellis > > > > call. Fits[subscripts] gives me the fits (or whatever) I want to plot > > for > > > > each panel. It is not clear to me how the panel layout information from > > > > panel.number(), etc. would be helpful here instead. Am I correct? -- or > > is > > > > there a smarter way to do this that I've missed? > > > > > > This is one of things that I think ggplot does better - it's much > > > easier to plot multiple data sources. I don't have many examples of > > > this yet, but the final example on > > > http://had.co.nz/ggplot2/geom_abline.html illustrates the basic idea. > > > > That's probably true. The Trellis approach is to define a plot by > > "data source" + "type of plot", whereas the ggplot approach (if I > > understand correctly) is to create a specification for the display > > (incrementally?) and then render it. Since the specification can be > > very general, the approach is very flexible. The downside is that you > > need to learn the language. > > > > On a philosophical note, I think the apparent limitations of Trellis > > in some (not all) cases is just due to the artificial importance given > > to data frames as the one true container for data. Now that we have > > proper multiple dispatch in S4, we can write methods that behave like > > traditional Trellis calls but work with more complex data structures. > > We have tried this in one bioconductor package (flowViz) with > > encouraging results. > > > > -Deepayan ______________________________________________ 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 and provide commented, minimal, self-contained, reproducible code.