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r.a.lowe1
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@ralowe1-10003
Last seen 8.0 years ago
Hi all,
I am trying to plot a sashimi plot for a RNA-seq experiment but whenever I use the sashimi type in Gviz it squashes the output either to PNG or to Quartz.
Any ideas on how to fix?
Updated with code example:
afrom <- 2960000
ato <- 3160000
alTrack <- AlignmentsTrack(system.file(package = "Gviz","extdata", "gapped.bam"), isPaired = TRUE)
bmt <- BiomartGeneRegionTrack(genome = "hg19", chromosome = "chr12", start = afrom, end = ato, filter = list(with_ox_refseq_mrna = TRUE), stacking = "dense")
plotTracks(c(bmt, alTrack, alTrack), from = afrom + 12700,to = afrom + 15200, chromosome = "chr12", type = c("coverage","sashimi"))
Thanks,
Rob
Can you please provide reproducible example of your code and your sessionInfo?
I have updated the question with reproducible example code.
SessionInfo below:
R version 3.2.4 (2016-03-10)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.11.3 (El Capitan)
locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
attached base packages:
[1] grid parallel stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] Gviz_1.14.5 GenomicRanges_1.22.4 GenomeInfoDb_1.6.3 IRanges_2.4.8 S4Vectors_0.8.11 BiocGenerics_0.16.1
loaded via a namespace (and not attached):
[1] Rcpp_0.12.4 RColorBrewer_1.1-2 futile.logger_1.4.1 plyr_1.8.3 XVector_0.10.0 GenomicFeatures_1.22.13
[7] bitops_1.0-6 futile.options_1.0.0 tools_3.2.4 zlibbioc_1.16.0 rpart_4.1-10 biomaRt_2.26.1
[13] digest_0.6.9 BSgenome_1.38.0 gtable_0.2.0 RSQLite_1.0.0 lattice_0.20-33 biovizBase_1.18.0
[19] DBI_0.3.1 gridExtra_2.2.1 cluster_2.0.3 rtracklayer_1.30.3 Biostrings_2.38.4 nnet_7.3-12
[25] Biobase_2.30.0 AnnotationDbi_1.32.3 XML_3.98-1.4 survival_2.38-3 BiocParallel_1.4.3 foreign_0.8-66
[31] Formula_1.2-1 latticeExtra_0.6-28 ggplot2_2.1.0 lambda.r_1.1.7 Rsamtools_1.22.0 scales_0.4.0
[37] Hmisc_3.17-2 matrixStats_0.50.1 GenomicAlignments_1.6.3 splines_3.2.4 dichromat_2.0-0 SummarizedExperiment_1.0.2
[43] colorspace_1.2-6 acepack_1.3-3.3 RCurl_1.95-4.8 munsell_0.4.3 VariantAnnotation_1.16.4