Error with repeat lines() in function

The problem was is that you were not return a value from the apply
function.  It was trying to store the result of the apply into an array and
there was no value.

See the line I added in your function.
__________________________________________________________
James Holtman        "What is the problem you are trying to solve?"
Executive Technical Consultant  --  Office of Technology, Convergys
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                      Sean Davis                                                                                                           
                      <sdavis2 at mail.nih.gov        To:       Uwe Ligges <ligges at statistik.uni-dortmund.de>                                 
                      >                            cc:       r-help <r-help at stat.math.ethz.ch>                                             
                      Sent by:                     Subject:  Re: [R] Error with repeat lines() in function                                 
                      r-help-bounces at stat.m                                                                                                
                      ath.ethz.ch                                                                                                          
                                                                                                                                           
                                                                                                                                           
                      09/24/2004 13:09                                                                                                     
                                                                                                                                           
                                                                                                                                           




Here is an example that seems to reproduce the error:

rf1 <- matrix(sort(abs(round(runif(4)*1000000))),nrow=1)
annot1 <- sort(abs(round(runif(193)*1000000)))
annot2 <- annot1 + 70
annot3 <- cbind(annot1,annot2)
rat2 <- rnorm(193)
rat1 <- rnorm(193)
plotter <-
function(annot,rat1,rat2,rf1,...) {
     par(las=2)
     xmax <- max(annot[,2])
     xmin <- min(annot[,1])
     par(mfrow=c(2,1))
     plot(annot[,1],rat1,type="l",xlab="",ylab="log2 Ratio",...)
     points(annot[,1],rat1)
     apply(rf1,1,function(z) {
       if (z[4]=="+") {
         color <- 'green'
         yoffset=1
       } else {
         color <- 'red'
         yoffset=-1
       }

lines(list(x=c(z[1],z[4]),y=c(-2-yoffset/10,-2-yoffset/
10)),lwd=2,col=color)

lines(list(x=c(z[2],z[3]),y=c(-2-yoffset/10,-2-yoffset/
10)),lwd=4,col=color)

1     #  fake a return value

     })
     abline(h=0,lty=2)
   }
plotter(annot3,rat1,rat2,rf1)
Error in ans[[1]] : subscript out of bounds

Enter a frame number, or 0 to exit
1:plotter(annot3, rat1, rat2, rf1)
2:apply(rf1, 1, function(z) {
Selection: 0

Sean Davis wrote:

I have a function that does some plotting.  I then add lines to the
plot.  If executed one line at a time, there is not a problem.  If I
execute the function, though, I get:
Error in ans[[1]] : subscript out of bounds
This always occurs after the second lines command, and doesn't happen
 with all of my data points (some do not have errors).  Any ideas?

Please give an example how to produce the error,
i.e. specify a very small toy example (including generated data and
the call to your function).
Many people on this list are quite busy these days and don't want to
think about how to call your function and invent an example ...

Uwe Ligges

Thanks,
Sean
 function(x,annot,rat1,rat2,rf,...) {
    par(las=2)
    wh <- which(annot[,5]==x)
    xmax <- max(annot[wh,4])
    xmin <- min(annot[wh,3])
    chr <- annot[wh,2][1]
    wh.rf <- rf$chrom==as.character(chr) & rf$txStart>xmin &
rf$txEnd<xmax
    par(mfrow=c(2,1))
    plot(annot[wh,3],rat1[wh],type="l",xlab="",ylab="log2
Ratio",main=x,...)
    points(annot[wh,3],rat1[wh])
    apply(rf[wh.rf,],1,function(z) {
      browser()
      if (z[4]=="+") {
        color <- 'green'
        yoffset=1
      } else {
        color <- 'red'
        yoffset=-1
      }
       lines(list(x=c(z[5],z[6]),y=c(-2-yoffset/10,-2-yoffset/
10)),lwd=2,col=color)
       lines(list(x=c(z[5],z[6]),y=c(-2-yoffset/10,-2-yoffset/
10)),lwd=2,col=color)
    })
    abline(h=0,lty=2)
}

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______________________________________________
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PLEASE do read the posting guide!
http://www.R-project.org/posting-guide.html