Sean Davis wrote:
Here is an example that seems to reproduce the error:
Well, debugging in apply() isn't funny and I'm tooo lazy at quarter past eight on a friday evening. Anyway, you can
(a) do it using a loop (which isn't that inefficient compared to the apply() approach), or
(b) the clever (vectorized) way that follows:
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)
yoffset <- ifelse(rf1[,4] == "+", 1, -1)
color <- ifelse(rf1[,4] == "+", "green", "red")
segments(rf1[,1], -2-yoffset/10, rf1[,4], -2-yoffset/ 10,
lwd=2, col=color)
segments(rf1[,2], -2-yoffset/10, rf1[,3], -2-yoffset/ 10,
lwd=4, col=color)abline(h=0,lty=2) }
Uwe Ligges
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)
})
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
On Sep 24, 2004, at 12:05 PM, Uwe Ligges wrote:
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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______________________________________________
[EMAIL PROTECTED] mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
______________________________________________ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
