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stianlagstad / chimeraviz

chimeraviz is an R package that automates the creation of chimeric RNA visualizations.
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plotFusionTranscriptWithProteinDomain function not found #13

Closed raunakms closed 6 years ago

raunakms commented 6 years ago

Got following error message:

?plotFusionTranscriptWithProteinDomain() Error in .helpForCall(topicExpr, parent.frame()) : no methods for 'plotFusionTranscriptWithProteinDomain' and no documentation for it as a function

stianlagstad commented 6 years ago

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.

raunakms commented 6 years ago

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

stianlagstad commented 6 years ago

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 :)