csijcs
commented
5 years ago Sorry, I should also mention that this is the command I am running:
plot_fusion(
+ fusion = fusion,
+ bamfile = bamfile,
+ edb = edb)
And the output of the parameters:
> edb
EnsDb for Ensembl:
|Backend: SQLite
|Db type: EnsDb
|Type of Gene ID: Ensembl Gene ID
|Supporting package: ensembldb
|Db created by: ensembldb package from Bioconductor
|script_version: 0.0.1
|Creation time: Fri Feb 22 11:30:47 2019
|ensembl_version: 95
|ensembl_host: unknown
|Organism: Homo_sapiens
|genome_build: GRCh38
|DBSCHEMAVERSION: 1.0
|source_file: Homo_sapiens.GRCh38.95.gtf
| No. of genes: 58735.
| No. of transcripts: 206601.>bamfile
[1] "/Users/csijcs/RHB5885_combined_junction_and_spanning_reads.bam"> fusion
[1] "Fusion object"
[1] "id: 525"
[1] "Fusion tool: starfusion"
[1] "Genome version: hg38"
[1] "Gene names: JARID2-HNRNPA2B1"
[1] "Chromosomes: chr6-chr7"
[1] "Strands: +,-"
[1] "In-frame?: NA"
stianlagstad
Love the program. I know this issue was brought up before (almost 1 year ago), but I don't see if there is a solution yet. I can make the fusion plot just fine, but there is no coverage shown. I am using STAR-fusion 1.4.0. to call fusions, and running R 3.5.2 on a Mac OS Mojave 10.14.2. I know you said previously that the tool does not yet support it, but I was hoping that by now it would. Can you please let me know?
Here is my sessioninfo: ` R version 3.5.2 (2018-12-20) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS Mojave 10.14.2
Matrix products: default BLAS: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib
locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages: [1] grid stats4 parallel stats graphics grDevices utils datasets methods base
other attached packages: [1] Rsamtools_1.34.1 BiocInstaller_1.32.1 chimeraviz_1.8.1 data.table_1.12.0 ensembldb_2.6.6 AnnotationFilter_1.6.0 GenomicFeatures_1.34.3 AnnotationDbi_1.44.0 Biobase_2.42.0 Gviz_1.26.4 GenomicRanges_1.34.0 GenomeInfoDb_1.18.2 Biostrings_2.50.2
[14] XVector_0.22.0 IRanges_2.16.0 S4Vectors_0.20.1 BiocGenerics_0.28.0
loaded via a namespace (and not attached): [1] ProtGenerics_1.14.0 bitops_1.0-6 matrixStats_0.54.0 bit64_0.9-7 RColorBrewer_1.1-2 progress_1.2.0 httr_1.4.0 tools_3.5.2 backports_1.1.3 DT_0.5
[11] R6_2.4.0 rpart_4.1-13 Hmisc_4.2-0 DBI_1.0.0 lazyeval_0.2.1 colorspace_1.4-0 nnet_7.3-12 tidyselect_0.2.5 gridExtra_2.3 prettyunits_1.0.2
[21] DESeq2_1.22.2 bit_1.1-14 curl_3.3 compiler_3.5.2 htmlTable_1.13.1 DelayedArray_0.8.0 rtracklayer_1.42.1 scales_1.0.0 checkmate_1.9.1 genefilter_1.64.0
[31] RCircos_1.2.0 stringr_1.4.0 digest_0.6.18 foreign_0.8-71 rmarkdown_1.11 base64enc_0.1-3 dichromat_2.0-0 pkgconfig_2.0.2 htmltools_0.3.6 BSgenome_1.50.0
[41] htmlwidgets_1.3 rlang_0.3.1 rstudioapi_0.9.0 RSQLite_2.1.1 gtools_3.8.1 BiocParallel_1.16.6 acepack_1.4.1 dplyr_0.8.0.1 VariantAnnotation_1.28.11 RCurl_1.95-4.11
[51] magrittr_1.5 GenomeInfoDbData_1.2.0 Formula_1.2-3 Matrix_1.2-15 Rcpp_1.0.0 munsell_0.5.0 yaml_2.2.0 stringi_1.3.1 SummarizedExperiment_1.12.0 zlibbioc_1.28.0
[61] org.Hs.eg.db_3.7.0 plyr_1.8.4 blob_1.1.1 crayon_1.3.4 lattice_0.20-38 splines_3.5.2 annotate_1.60.0 hms_0.4.2 locfit_1.5-9.1 knitr_1.21
[71] pillar_1.3.1 geneplotter_1.60.0 biomaRt_2.38.0 XML_3.98-1.17 glue_1.3.0 evaluate_0.13 biovizBase_1.30.1 latticeExtra_0.6-28 BiocManager_1.30.4 org.Mm.eg.db_3.7.0
[81] gtable_0.2.0 purrr_0.3.0 assertthat_0.2.0 ggplot2_3.1.0 xfun_0.5 xtable_1.8-3 ArgumentCheck_0.10.2 survival_2.43-3 tibble_2.0.1 GenomicAlignments_1.18.1
[91] memoise_1.1.0 cluster_2.0.7-1 BiocStyle_2.10.0
`