Dear bioc-sig-sequencing,
I received the following error message while running code from slide 17 from
the workshop lab CoverageEDA.pdf, 01/29/10 in Seattle,
(http://www.bioconductor.org/help/course-materials/2010/SeattleJan10/day3/CoverageEDA.pdf)
> plotCoverage <-
+ function (x, chrom, start = 1, end = length(x[[chrom]]), col = "blue",
+ xlab = "Index", ylab = "Coverage", main = chrom)
+ {
+ xWindow <- as.vector(window(x[[chrom]], start, end))
+ x <- start:end
+ xlim <- c(start, end)
+ ylim <- c(0, max(xWindow))
+ plot(x = start, y = 0, xlim = xlim, ylim = ylim, xlab = xlab,
+ ylab = ylab, main = main, type = "n")
+ polygon(c(start, x, end), c(0, xWindow, 0), col = col)
+ }
> plotCoverage(cov.arabtest1_s8, "chr1")
Error in polygon(c(start, x, end), c(0, xWindow, 0), col = col) :
X11 fatal IO error: please save work and shut down R
> sessionInfo()
R version 2.12.0 Under development (unstable) (2010-08-02 r52661)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C
[3] LC_TIME=en_US.utf8 LC_COLLATE=en_US.utf8
[5] LC_MONETARY=C LC_MESSAGES=en_US.utf8
[7] LC_PAPER=en_US.utf8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] chipseq_0.99.1 BSgenome_1.17.6 ShortRead_1.7.11
[4] Rsamtools_1.1.11 lattice_0.18-8 Biostrings_2.17.27
[7] GenomicRanges_1.1.20 IRanges_1.7.15
loaded via a namespace (and not attached):
[1] Biobase_2.9.0 grid_2.12.0 hwriter_1.2
>
The plot works fine with the 2.11 release vesion of R. This is a linux Ubuntu
laptop running 10.04, 8 Gb ram.
Thanks,
P. Terry
[email protected]
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