Comments (3)
Hi! Thank you for your interest in chimeraviz. Could you please run sessionInfo()
and paste the result here? The problem might be that you're using the previous version of Bioconductor and thus the old version of chimeraviz. Here, under "Update Installed Bioconductor Packages", are instructions for how to upgrade Bioconductor and the package you've installed.
from chimeraviz.
sessionInfo()
R version 3.4.1 (2017-06-30)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C LC_TIME=English_United States.1252
attached base packages:
[1] grid stats4 parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] chimeraviz_1.0.4 ensembldb_2.0.4 AnnotationFilter_1.0.0 GenomicFeatures_1.28.5 AnnotationDbi_1.38.2 Biobase_2.36.2
[7] Gviz_1.20.0 GenomicRanges_1.28.6 GenomeInfoDb_1.12.3 Biostrings_2.44.2 XVector_0.16.0 IRanges_2.10.5
[13] S4Vectors_0.14.7 BiocGenerics_0.22.1
loaded via a namespace (and not attached):
[1] ProtGenerics_1.8.0 bitops_1.0-6 matrixStats_0.52.2 bit64_0.9-7
[5] RColorBrewer_1.1-2 httr_1.3.1 rprojroot_1.2 tools_3.4.1
[9] backports_1.1.1 R6_2.2.2 DT_0.2 rpart_4.1-11
[13] Hmisc_4.0-3 DBI_0.7 lazyeval_0.2.1 colorspace_1.3-2
[17] nnet_7.3-12 gridExtra_2.3 bit_1.1-12 curl_3.0
[21] compiler_3.4.1 htmlTable_1.9 DelayedArray_0.2.7 rtracklayer_1.36.6
[25] scales_0.5.0 checkmate_1.8.5 readr_1.1.1 RCircos_1.2.0
[29] stringr_1.2.0 digest_0.6.12 Rsamtools_1.28.0 foreign_0.8-69
[33] rmarkdown_1.6 base64enc_0.1-3 dichromat_2.0-0 pkgconfig_2.0.1
[37] htmltools_0.3.6 BSgenome_1.44.2 htmlwidgets_0.9 rlang_0.1.4
[41] RSQLite_2.0 BiocInstaller_1.26.1 shiny_1.0.5 BiocParallel_1.10.1
[45] acepack_1.4.1 VariantAnnotation_1.22.3 RCurl_1.95-4.8 magrittr_1.5
[49] GenomeInfoDbData_0.99.0 Formula_1.2-2 Matrix_1.2-10 Rcpp_0.12.13
[53] munsell_0.4.3 stringi_1.1.5 yaml_2.1.14 SummarizedExperiment_1.6.5
[57] zlibbioc_1.22.0 org.Hs.eg.db_3.4.1 plyr_1.8.4 AnnotationHub_2.8.3
[61] blob_1.1.0 lattice_0.20-35 splines_3.4.1 hms_0.3
[65] knitr_1.17 biomaRt_2.32.1 XML_3.98-1.9 evaluate_0.10.1
[69] biovizBase_1.24.0 latticeExtra_0.6-28 data.table_1.10.4-3 httpuv_1.3.5
[73] gtable_0.2.0 ggplot2_2.2.1 mime_0.5 xtable_1.8-2
[77] survival_2.41-3 tibble_1.3.4 GenomicAlignments_1.12.2 memoise_1.1.0
[81] cluster_2.0.6 interactiveDisplayBase_1.14.0 BiocStyle_2.4.1
from chimeraviz.
It looks like you're using an older version of R. Try to install version 3.4.2 so that you can install Bioconductor 2.6. That should get you chimeraviz 1.4.0, which has the plot you're interested in :)
from chimeraviz.
Related Issues (20)
- Question: what are the red bands on the chromosome? HOT 4
- Assignment to global environment HOT 1
- plot_fusion function not finding "SPFQ" or "CADM2" transcripts in an edb object that has them. HOT 2
- Why is it impossible to use plot_fusion_transcript_with_protein_domain without a BAM file? HOT 1
- Support ChimPipe HOT 1
- coverage issue in plot_fusion_separate HOT 2
- How to make fusioncatcher data compatible to chimeraviz HOT 4
- Chromosome not labeled correctly? HOT 4
- Support Fusion-Bloom
- Travis build fails
- plot_fusion_transcript_with_protein_domain(): error plotting upstream domains HOT 2
- Failed to create reference fasta file HOT 4
- How to input STAR-SEQR output? HOT 1
- Dependency on deprecated ArgumentCheck CRAN package HOT 1
- 2 question with chimeraviz HOT 3
- Custom genomes HOT 2
- Error during the execution of plot_fusion HOT 5
- Failed to create EnsDb HOT 1
- No coverage data for plot_fusion HOT 2
- Fusion transcript plot with protein domain annotations HOT 1
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