hi,
ive proccessed chromosomeExplorer for all the chromosomes and i get
many plots but also the error (although it doesnt stop cause of it)...
if i do the traceback i get this
>traceback()
32: unlist(args)
31: as.list(unlist(args))
30: par("lwd")
29: int_abline(a = a, b = b, h = h, v = v, untf = untf, ...)
28: abline(h = log2(level), col = "blue", lty = 2)
27: withCallingHandlers(expr, warning = function(w) invokeRestart
("muffleWarning"))
26: suppressWarnings({
newPlot(this, xlim = xlim, ylim = ylim, flavor = "ce", unit =
unit,
...)
drawXAxisRuler(xrange = c(0, nbrOfBases)/10^unit, ticksBy =
ticksBy)
if (!identical(this$.plotCytoband, FALSE)) {
drawCytoband(this, chromosome = chromosome, unit = unit)
}
cnLevels <- c(1/2, 1, 3/2)
for (level in cnLevels) {
abline(h = log2(level), col = "blue", lty = 2)
}
rawCns <- extractRawCopyNumbers(fit)
verbose && print(verbose, rawCns, level = -50)
n <- nbrOfLoci(rawCns, na.rm = TRUE)
stext(text = sprintf("n=%d", n), side = 4, pos = 0, line = 0,
cex = 0.8)
pointsRawCNs(fit, unit = unit, ...)
cnRegions <- extractCopyNumberRegions(fit)
verbose && print(verbose, cnRegions, level = -50)
drawLevels(cnRegions, lwd = 4, col = "black", xScale =
1/10^unit)
drawExtraAnnotations(fit)
onFitAddGenotypeCalls(fit, callList = callList, arrayName =
arrayName,
resScale = 10^unit * resScale, ...)
})
25: doTryCatch(return(expr), name, parentenv, handler)
24: tryCatchOne(expr, names, parentenv, handlers[[1]])
23: tryCatchList(expr, classes, parentenv, handlers)
22: tryCatch({
verbose && enter(verbose, "Plotting graph")
opar <- par(xaxs = "r")
suppressWarnings({
newPlot(this, xlim = xlim, ylim = ylim, flavor = "ce",
unit = unit, ...)
drawXAxisRuler(xrange = c(0, nbrOfBases)/10^unit, ticksBy
= ticksBy)
if (!identical(this$.plotCytoband, FALSE)) {
drawCytoband(this, chromosome = chromosome, unit =
unit)
}
cnLevels <- c(1/2, 1, 3/2)
for (level in cnLevels) {
abline(h = log2(level), col = "blue", lty = 2)
}
rawCns <- extractRawCopyNumbers(fit)
verbose && print(verbose, rawCns, level = -50)
n <- nbrOfLoci(rawCns, na.rm = TRUE)
stext(text = sprintf("n=%d", n), side = 4, pos = 0, line =
0,
cex = 0.8)
pointsRawCNs(fit, unit = unit, ...)
cnRegions <- extractCopyNumberRegions(fit)
verbose && print(verbose, cnRegions, level = -50)
drawLevels(cnRegions, lwd = 4, col = "black", xScale =
1/10^unit)
drawExtraAnnotations(fit)
onFitAddGenotypeCalls(fit, callList = callList, arrayName
= arrayName,
resScale = 10^unit * resScale, ...)
})
stext(chipType, side = 4, pos = 1, line = 0, cex = 0.8)
verbose && exit(verbose)
}, error = function(ex) {
print(ex)
}, finally = {
par(opar)
if (!imageFormat %in% c("screen", "current"))
dev.off()
})
21: doTryCatch(return(expr), name, parentenv, handler)
20: tryCatchOne(expr, names, parentenv, handlers[[1]])
19: tryCatchList(expr, classes, parentenv, handlers)
18: tryCatch({
arrayFullName <- gsub("^(.*),chr[0-9][0-9].*$", "\\1",
fullname)
arrayName <- gsub("^([^,]*).*$", "\\1", arrayFullName)
nbrOfBases <- genome$nbrOfBases[chromosome]
widthMb <- nbrOfBases/10^unit
if (is.null(xlim)) {
xlim <- c(0, getChromosomeLength(chromosome))/10^unit
}
verbose && enter(verbose, sprintf("Plotting %s for chromosome
%02d [%.2fMB]",
arrayName, chromosome, widthMb))
for (zz in seq(along = zooms)) {
zoom <- zooms[zz]
imgName <- sprintf("%s,chr%02d,x%04d.%s", arrayFullName,
chromosome, zoom, imageFormat)
pathname <- filePath(path, imgName)
pathname <- gsub(" ", "_", pathname)
if (!imageFormat %in% c("screen", "current")) {
if (skip && isFile(pathname)) {
next
}
}
ticksBy <- 10^ceiling(log10(pixelsPerTick/(zoom *
pixelsPerMb)))
width <- round(zoom * widthMb * pixelsPerMb + sum
(xmargin))
verbose && printf(verbose, "Pathname: %s\n", pathname)
verbose && printf(verbose, "Dimensions: %dx%d\n", width,
height)
verbose && printf(verbose, "Ticks by: %f\n", ticksBy)
if (!is.null(plotDev))
plotDev(pathname, width = width, height = height)
tryCatch({
verbose && enter(verbose, "Plotting graph")
opar <- par(xaxs = "r")
suppressWarnings({
newPlot(this, xlim = xlim, ylim = ylim, flavor =
"ce",
unit = unit, ...)
drawXAxisRuler(xrange = c(0, nbrOfBases)/10^unit,
ticksBy = ticksBy)
if (!identical(this$.plotCytoband, FALSE)) {
drawCytoband(this, chromosome = chromosome,
unit = unit)
}
cnLevels <- c(1/2, 1, 3/2)
for (level in cnLevels) {
abline(h = log2(level), col = "blue", lty = 2)
}
rawCns <- extractRawCopyNumbers(fit)
verbose && print(verbose, rawCns, level = -50)
n <- nbrOfLoci(rawCns, na.rm = TRUE)
stext(text = sprintf("n=%d", n), side = 4, pos =
0,
line = 0, cex = 0.8)
pointsRawCNs(fit, unit = unit, ...)
cnRegions <- extractCopyNumberRegions(fit)
verbose && print(verbose, cnRegions, level = -50)
drawLevels(cnRegions, lwd = 4, col = "black",
xScale = 1/10^unit)
drawExtraAnnotations(fit)
onFitAddGenotypeCalls(fit, callList = callList,
arrayName = arrayName, resScale = 10^unit *
resScale, ...)
})
stext(chipType, side = 4, pos = 1, line = 0, cex =
0.8)
verbose && exit(verbose)
}, error = function(ex) {
print(ex)
}, finally = {
par(opar)
if (!imageFormat %in% c("screen", "current"))
dev.off()
})
}
}, error = function(ex) {
cat("ERROR caught in ", hookName, "():\n", sep = "")
print(ex)
}, finally = {
gc <- gc()
verbose && print(verbose, gc)
verbose && exit(verbose)
})
17: fcn(...)
16: doTryCatch(return(expr), name, parentenv, handler)
15: tryCatchOne(expr, names, parentenv, handlers[[1]])
14: tryCatchList(expr, classes, parentenv, handlers)
13: tryCatch({
result <- fcn(...)
tmp[["result"]] <- result
failedHooks[kk] <- FALSE
}, error = function(ex) {
tmp[["exception"]] <<- ex
})
12: callHooks.list(hooks, ...)
11: callHooks(hooks, ...)
10: callHooks.default(hookName, fit = fit, chromosome = chr, fullname
= fullname)
9: callHooks(hookName, fit = fit, chromosome = chr, fullname =
fullname)
8: fit.CopyNumberSegmentationModel(this, ..., .retResults = FALSE,
verbose = verbose)
7: fit(this, ..., .retResults = FALSE, verbose = verbose)
6: plot.CopyNumberSegmentationModel(model, path = path, imageFormat =
"png",
plotband = plotband, arrays = arrays, ...)
5: plot(model, path = path, imageFormat = "png", plotband = plotband,
arrays = arrays, ...)
4: writeGraphs.ChromosomeExplorer(this, arrays = arrays, chromosomes =
chromosomes,
..., verbose = less(verbose))
3: writeGraphs(this, arrays = arrays, chromosomes = chromosomes,
..., verbose = less(verbose))
2: process.ChromosomeExplorer(ce, verbose = verbose)
1: process(ce, verbose = verbose)
ive also tried with the R v2.8.0patched and it gives the same error...
thanks,
maría
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