[R] Help with ooplot(gplots) and error bars

[Frank E Harrell Jr]

Jean-Louis Abitbol wrote:
> Dear Pr Harrel,
> 
> Thanks for your help at this occasion as well as for previous questions
> to the list.
> 
> I just looked at the example in your intro doc.
> 
> However I am dealing with proportions (ie % of patients responding to a
> given treatment).
> 
> In this case I am not sure I can use summarize and then the xYplot.
> 
> I am not aware of R graphing tools that can deal directly with
> proportions adding CI not to mention producing by factor/trellis plots.
> 
> This is why I why trying to do it "by hand" (using binconf) with ooplot,
> without much success I am afraid. 
> 
> Best regards,
> 
> JL Abitbol, MD

Jean-Louis,

Here is an example.

# Plot proportions and their Wilson confidence limits
set.seed(3)
d <- expand.grid(continent=c('USA','Europe'), year=1999:2001,
                  reps=1:100)
# Generate binary events from a population probability of 0.2
# of the event, same for all years and continents
d$y <- ifelse(runif(6*100) <= .2, 1, 0)
s <- with(d,
           summarize(y, llist(continent,year),
                     function(y) {
                      n <- sum(!is.na(y))
                      s <- sum(y, na.rm=T)
                      binconf(s, n)
                     }, type='matrix')
)

Dotplot(year ~ Cbind(y) | continent,  data=s, ylab='Year',
         xlab='Probability')

I did have to temporarily override a function in Hmisc to fix a problem. 
  This will be corrected in an upcoming release of Hmisc:

mApply <- function(X, INDEX, FUN=NULL, ..., simplify=TRUE) {
## Matrix tapply
## X: matrix with n rows; INDEX: vector or list of vectors of length n
## FUN: function to operate on submatrices of x by INDEX
## ...: arguments to FUN; simplify: see sapply
## Modification of code by Tony Plate <tplate at blackmesacapital.com> 10Oct02
## If FUN returns more than one number, mApply returns a matrix with
## rows corresponding to unique values of INDEX
nr <- nrow(X)
if(!length(nr)) {  ## X not a matrix
   r <- tapply(X, INDEX, FUN, ..., simplify=simplify)
   if(is.matrix(r)) r <- drop(t(r)) else
   if(simplify && is.list(r))
     r <- drop(matrix(unlist(r), nrow=length(r),
                      dimnames=list(names(r),names(r[[1]])), byrow=TRUE))
} else {
   idx.list <- tapply(1:nr, INDEX, c)
   r <- sapply(idx.list, function(idx,x,fun,...) 
fun(x[idx,,drop=FALSE],...),
               x=X, fun=FUN, ..., simplify=simplify)
   if(simplify) r <- drop(t(r))
}
dn <- dimnames(r)
if(length(dn) && !length(dn[[length(dn)]])) {
   fx <- FUN(X,...)
   dnl <- if(length(names(fx))) names(fx) else dimnames(fx)[[2]]
   dn[[length(dn)]] <- dnl
   dimnames(r) <- dn
}

if(simplify && is.list(r) && is.array(r)) {

   ll <- sapply(r, length)
   maxl <- max(ll)
   empty <- (1:length(ll))[ll==0]
   for(i in empty) r[[i]] <- rep(NA, maxl)
   ## unlist not keep place for NULL entries for nonexistent categories
   first.not.empty <- ((1:length(ll))[ll > 0])[1]
   nam <- names(r[[first.not.empty]])
   dr <- dim(r)

   r <- aperm(array(unlist(r), dim=c(maxl,dr),
                    dimnames=c(list(nam),dimnames(r))),
              c(1+seq(length(dr)), 1))
}
r
}



Frank

> 
> On Sun, 21 Nov 2004 07:48:58 -0500, "Frank E Harrell Jr"
> <f.harrell at vanderbilt.edu> said:
> 
>>Jean-Louis Abitbol wrote:
>>
>>>Dear All
>>>
>>>I am trying to graph a proportion and CI95% by a factor with ooplot (any
>>>other better solution ?)
>>>
>>>It works well until I try to add the confidence interval.
>>>
>>>this is the error message and and a description of the data:
>>>  
>>> > dat1
>>>        PointEst
>>>TT1   1      3.6
>>>TT2   2      5.0
>>>TT3   3      5.8
>>>TT4   4     11.5
>>>TT5   5      7.5
>>>TT5   6      8.7
>>>TT7   7     17.4
>>>
>>>
>>>>dat2
>>>
>>>        Lower
>>>TT1   1   1.0
>>>TT2   2   2.2
>>>TT3   3   2.7
>>>TT4   4   6.7
>>>TT5   5   3.9
>>>TT5   6   4.6
>>>TT7   7  11.5
>>>
>>>
>>>>dat3
>>>
>>>        Upper
>>>TT1   1  12.3
>>>TT2   2  11.2
>>>TT3   3  12.1
>>>TT4   4  19.1
>>>TT5   5  14.2
>>>TT5   6  15.6
>>>TT7   7  25.6
>>>
>>>
>>>>ooplot(dat1,type="barplot",col=rich.colors(7,"temperature"),names.arg=c("X","Y","Z","A","B","C","D"),plot.ci=T,
>>>
>>>+ ci.l=dat2,ci.u=dat3, xlab="Treatment", ylab="Percent Normalized
>>>Patients")
>>>Error in ooplot.default(dat1, type = "barplot", col = rich.colors(7,
>>>"temperature"),  : 
>>>        'height' and 'ci.u' must have the same dimensions.
>>>
>>>I have tried various ways of supplying ci.l and ci.u (including a
>>>vector)
>>>
>>>
>>>Thanks for the help that anyone can bring,
>>>
>>>Regards, JL
>>
>>One way is to look at the examples for Dotplot in the Hmisc package. 
>>Those examples display bootstrap percentile confidence intervals for a
>>mean.
>>
>>-- 
>>Frank E Harrell Jr   Professor and Chair           School of Medicine
>>                      Department of Biostatistics   Vanderbilt University
> 
>