On 09/05/2013 10:02 AM, Dan Tenenbaum wrote: > On Thu, Sep 5, 2013 at 9:51 AM, Jager, Dominik <jager.9 at="" osu.edu=""> wrote: >> Hi, >> >> Sorry for the double post! >> >> I'm a R and Bioconductor beginner currently trying to get myself familiar with the Gviz package, >> thus "playing" around with the examples provided in the package manual. I'm using >> Bioconductor version 2.12 and this is what is happening: >> >>> library(GenomicRanges) >>> library(Gviz) >>> data(cpgIslands) >>> chr <- as.character(unique(seqnames(cpgIslands))) >>> gen <- genome(cpgIslands) >>> AnnotationTrack(cpgIslands, name = "CpG") -> atrack >>> GenomeAxisTrack() -> gtrack >>> plotTracks(atrack, gtrack) >> > > I don't see this code in either the manual pages or the vignette of Gviz 1.4.5. > Furthermore, this code doesn't look right. Assignments go on the left, > and use ",-", so instead of > > GenomeAxisTrack() -> gtrack > > You want to say: > > gtrack <- GenomeAxisTrack() actually, one of those fun things about R is that left and right assignments are both defined x <- 1 -> y I think the correct syntax for the final line is plotTracks(list(atrack, gtrack)) Martin > > I suggest that you copy and paste the example you're interested in, > and then make one small change at a time until you get it to do what > you want. > > Dan > > > >> Fehler in rep(no, length.out = length(ans)) : >> attempt to replicate an object of type 'S4' >> >> Further information: >> >> -------------------------------------------- >>> traceback() >> 8: ifelse(is.null(from), -Inf, from) >> 7: ifelse(is.null(from), -Inf, from) >> 6: .local(x, ...) >> 5: FUN(X[[1L]], ...) >> 4: FUN(X[[1L]], ...) >> 3: lapply(trackList, subset, from = from, to = to, chromosome = chromosome, >> sort = FALSE, stacks = FALSE, use.defaults = FALSE) >> 2: lapply(trackList, subset, from = from, to = to, chromosome = chromosome, >> sort = FALSE, stacks = FALSE, use.defaults = FALSE) >> 1: plotTracks(atrack, gtrack) >> >> ----------------------------------------------------- >> >>> sessionInfo() >> R version 3.0.1 (2013-05-16) >> Platform: x86_64-pc-linux-gnu (64-bit) >> >> locale: >> [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 >> [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8 LC_PAPER=C LC_NAME=C >> [9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] parallel grid stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] GenomicRanges_1.12.5 IRanges_1.18.3 BiocGenerics_0.6.0 Gviz_1.4.5 BiocInstaller_1.10.3 >> >> loaded via a namespace (and not attached): >> [1] AnnotationDbi_1.22.6 Biobase_2.20.1 biomaRt_2.16.0 Biostrings_2.28.0 biovizBase_1.8.1 >> [6] bitops_1.0-6 BSgenome_1.28.0 cluster_1.14.4 colorspace_1.2-2 DBI_0.2-7 >> [11] dichromat_2.0-0 GenomicFeatures_1.12.3 Hmisc_3.12-2 labeling_0.2 lattice_0.20-23 >> [16] munsell_0.4.2 plyr_1.8 RColorBrewer_1.0-5 RCurl_1.95-4.1 rpart_4.1-3 >> [21] Rsamtools_1.12.4 RSQLite_0.11.4 rtracklayer_1.20.4 scales_0.2.3 stats4_3.0.1 >> [26] stringr_0.6.2 tools_3.0.1 XML_3.98-1.1 zlibbioc_1.6.0 >> ------------------------------------------------ >> >> Thanks for you help! >> >> Dominik >> >> >> [The Ohio State University] >> Dr. Dominik J?ger >> Biological Sciences Department of Microbiology >> 405 Biological Science Building | 484 West 12th Avenue Columbus, OH 43210 >> (614)-682-6890 Office >> jager.9 at osu.edu<mailto:jager.9 at="" osu.edu=""> osu.edu<http: osu.edu=""> >> >> [[alternative HTML version deleted]] >> >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793