stianlagstad
commented
5 years ago Hi @fmarois. Thank you for your interest in chimeraviz :) While in some functions the bam/bedfile is optional, it is a requried parameter for plot_fusion and for plot_fusion_transcript_with_protein_domain.
Hello, Here is the issue i am facing: when I try to "plotFusion" or "plotFusionTranscriptWithProteinDomain" without providing a bam file I get an error. Here is the reproducible code and the error: ` if(!exists("defuse833ke")) defuse833ke <- system.file( "extdata", "defuse_833ke_results.filtered.tsv", package = "chimeraviz")
fusions <- importDefuse(defuse833ke, "hg19", 1)
fusion <- getFusionById(fusions, 5267) if(!exists("edbSqliteFile")) edbSqliteFile <- system.file( "extdata", "Homo_sapiens.GRCh37.74.sqlite", package="chimeraviz")
edb <- ensembldb::EnsDb(edbSqliteFile)
plotFusion( fusion = fusion, edb = edb, nonUCSC = TRUE)
Error: .validatePlotFusionParams(fusion, edb, bamfile, whichTranscripts, ylim, nonUCSC, reduceTranscripts, bedgraphfile)
1: Either 'bamfile' or 'bedgraphfile' must be given ` Is this normal, I saw in your vignette (and your code) that the coverage seems optional, am I mistaken?
fusion-finder: FusionCatcher 0.99.7c beta
`
Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1 LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1
locale: [1] LC_CTYPE=en_CA.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_CA.UTF-8 LC_COLLATE=en_CA.UTF-8
[5] LC_MONETARY=en_CA.UTF-8 LC_MESSAGES=en_CA.UTF-8
[7] LC_PAPER=en_CA.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C
attached base packages: [1] grid stats4 parallel stats graphics grDevices utils
[8] datasets methods base
other attached packages: [1] chimeraviz_1.4.3 ensembldb_2.2.2 AnnotationFilter_1.2.0 [4] GenomicFeatures_1.30.3 AnnotationDbi_1.40.0 Biobase_2.38.0
[7] Gviz_1.22.3 GenomicRanges_1.30.3 GenomeInfoDb_1.14.0
[10] Biostrings_2.46.0 XVector_0.18.0 IRanges_2.12.0
[13] S4Vectors_0.16.0 BiocGenerics_0.24.0
loaded via a namespace (and not attached): [1] ProtGenerics_1.10.0 bitops_1.0-6
[3] matrixStats_0.54.0 bit64_0.9-7
[5] RColorBrewer_1.1-2 progress_1.2.0
[7] httr_1.3.1 rprojroot_1.3-2
[9] tools_3.4.4 backports_1.1.2
[11] DT_0.5 R6_2.3.0
[13] rpart_4.1-13 Hmisc_4.1-1
[15] DBI_1.0.0 lazyeval_0.2.1
[17] colorspace_1.3-2 nnet_7.3-12
[19] tidyselect_0.2.5 gridExtra_2.3
[21] prettyunits_1.0.2 RMySQL_0.10.15
[23] curl_3.2 bit_1.1-14
[25] compiler_3.4.4 htmlTable_1.12
[27] DelayedArray_0.4.1 rtracklayer_1.38.3
[29] scales_1.0.0 checkmate_1.8.5
[31] readr_1.1.1 RCircos_1.2.0
[33] stringr_1.3.1 digest_0.6.18
[35] Rsamtools_1.30.0 foreign_0.8-71
[37] rmarkdown_1.10 base64enc_0.1-3
[39] dichromat_2.0-0 pkgconfig_2.0.2
[41] htmltools_0.3.6 BSgenome_1.46.0
[43] htmlwidgets_1.3 rlang_0.3.0.1
[45] rstudioapi_0.8 RSQLite_2.1.1
[47] BiocInstaller_1.28.0 shiny_1.2.0
[49] bindr_0.1.1 BiocParallel_1.12.0
[51] acepack_1.4.1 dplyr_0.7.8
[53] VariantAnnotation_1.24.5 RCurl_1.95-4.11
[55] magrittr_1.5 GenomeInfoDbData_1.0.0
[57] Formula_1.2-3 Matrix_1.2-15
[59] Rcpp_1.0.0 munsell_0.5.0
[61] stringi_1.2.4 yaml_2.2.0
[63] SummarizedExperiment_1.8.1 zlibbioc_1.24.0
[65] org.Hs.eg.db_3.5.0 plyr_1.8.4
[67] AnnotationHub_2.10.1 blob_1.1.1
[69] promises_1.0.1 crayon_1.3.4
[71] lattice_0.20-38 splines_3.4.4
[73] hms_0.4.2 knitr_1.20
[75] pillar_1.3.0 biomaRt_2.34.2
[77] XML_3.98-1.16 glue_1.3.0
[79] evaluate_0.12 biovizBase_1.26.0
[81] latticeExtra_0.6-28 data.table_1.11.8
[83] httpuv_1.4.5 gtable_0.2.0
[85] purrr_0.2.5 assertthat_0.2.0
[87] ggplot2_3.1.0 mime_0.6
[89] xtable_1.8-3 later_0.7.5
[91] ArgumentCheck_0.10.2 survival_2.43-1
[93] tibble_1.4.2 GenomicAlignments_1.14.2
[95] memoise_1.1.0 bindrcpp_0.2.2
[97] cluster_2.0.7-1 interactiveDisplayBase_1.16.0 [99] BiocStyle_2.6.1 ` OS : Ubuntu 18.04.1 LTS (Bionic Beaver)
Francois
PS. Thank you for chimeraviz