Skip to content

histogram method for S4 class.

3 messages · Deepayan Sarkar, Ernesto Jardim

Original
Ernesto Jardim
# 
Hi,

I'm trying to develop an histogram method for a class called "FLQuant"
which is used by the package FLCore (http://flr-project.org). FLQuant is
an extension to "array". There is an as.data.frame method that coerces
flquant into a data.frame suitable for lattice plotting. The problem is
that when I coerce the object and plot it after it works but if the
method is applied within the histogram method it does not work. See the
code below (the FLCore package is here
http://prdownloads.sourceforge.net/flr/FLCore_1.0-1.tar.gz?download)
Loading required package: lattice
Error in inherits(x, "factor") : Object "x" not found
The catch.n slot is a FLQuant object and the code for histogram is the
following

setMethod("histogram", signature(formula="formula", data="FLQuant"),
    function (formula, data = parent.frame(), allow.multiple =
is.null(groups) || outer,
        outer = FALSE, auto.key = FALSE, aspect = "fill", panel =
"panel.histogram", prepanel = NULL,
        scales = list(), strip = TRUE, groups = NULL, xlab, xlim, ylab,
ylim,
        type = c("percent", "count", "density"),
        nint = if (is.factor(x)) length(levels(x)) else
round(log2(length(x)) + 1),
        endpoints = extend.limits(range(x[!is.na(x)]), prop = 0.04),
        breaks = if (is.factor(x)) seq(0.5, length = length(levels(x)) +
1) else do.breaks(endpoints, nint),
        equal.widths = TRUE, drop.unused.levels =
lattice.getOption("drop.unused.levels"), ...,
        default.scales = list(), subscripts = !is.null(groups), subset =
TRUE) {

        qdf <- as.data.frame(data)

        histogram(formula, data = qdf, allow.multiple = allow.multiple,
outer = outer,
            auto.key = auto.key, aspect = aspect, panel = panel,
prepanel = prepanel, scales = scales,
            strip = strip, groups = groups, xlab=xlab, xlim=xlim,
ylab=ylab, ylim=ylim, type = type,
            nint = nint, endpoints = endpoints, breaks = breaks,
equal.widths = equal.widths,
            drop.unused.levels = drop.unused.levels, ..., default.scales
= default.scales,
            subscripts = subscripts, subset = subset)
    }
)


Any ideas ?

Thanks

EJ
1 day later
Deepayan Sarkar
#
On 8/24/05, ernesto <ernesto at ipimar.pt> wrote:
[I'm CC-ing to r-devel, please post follow-ups there]

What version of lattice are you using? Please use the latest one, in
which histogram is an S3 generic, with only one argument, formula. The
eventual solution to your problem may involve changing that, but the
first question to ask is whether any other formula makes sense in your
context (if not, I would rather keep one argument and dispatch on
signature(formula = "FLQuant").

Disclaimer: I haven't actually had time to check out FLCore yet, I
will as soon as I can.

Deepayan
Ernesto Jardim
#
Deepayan Sarkar wrote:

            

      
      
      
    

        
Hi,

I've installed the version that is distributed with R-2.1.1, 0.11-8. I 
see there's a new version now so I'll install it and check the results. 
I've developed the code a little more using the approach you use for 
dotplot (see below) and I know where the problem is now. I'm not able to 
pass the argument nint, breaks and endpoints to the function call. I 
guess the problem is my programming skils :-(

Thanks

EJ

ps: I'm not a subscriber of r-devel so I guess I'm not able to post 
there, anyway I'm CC-ing there too.



setMethod("histogram", signature(formula="formula", data="FLQuant"), 
function (formula, data = parent.frame(), allow.multiple = 
is.null(groups) || outer, outer = FALSE, auto.key = FALSE, aspect = 
"fill", panel = "panel.histogram", prepanel = NULL, scales = list(), 
strip = TRUE, groups = NULL, xlab, xlim, ylab, ylim, type = c("percent", 
"count", "density"), nint = if (is.factor(x)) length(levels(x)) else 
round(log2(length(x)) + 1), endpoints = 
extend.limits(range(x[!is.na(x)]), prop = 0.04), breaks = if 
(is.factor(x)) seq(0.5, length = length(levels(x)) + 1) else 
do.breaks(endpoints, nint), equal.widths = TRUE, drop.unused.levels = 
lattice.getOption("drop.unused.levels"), ..., default.scales = list(), 
subscripts = !is.null(groups), subset = TRUE) {

# need to develop further, at the moment is not possible to control 
nint, breaks and endpoints.

data <- as.data.frame(data)

dots <- list(...)

groups <- eval(substitute(groups), data, parent.frame())
subset <- eval(substitute(subset), data, parent.frame())

call.list <- c(list(formula = formula, data = data, groups = groups, 
subset = subset, allow.multiple = allow.multiple, outer = outer, 
auto.key = auto.key, aspect = aspect, panel = panel, prepanel = 
prepanel, scales = scales, strip = strip, type = type, equal.widths = 
equal.widths, drop.unused.levels = drop.unused.levels, default.scales = 
default.scales, subscripts = subscripts), dots)

# include xlab & co if existent
if(!missing(xlab)) call.list$xlab <- xlab
if(!missing(ylab)) call.list$ylab <- ylab
if(!missing(xlim)) call.list$xlim <- xlim
if(!missing(ylim)) call.list$ylim <- ylim

ans <- do.call("histogram", call.list)
ans$call <- match.call()
ans

})