Entering edit mode
Hi guys,
I'm following the vignette to create a circular plot
ggbio()+ circle(myGR, geom = "link", linked.to = "toRegion", aes(color = dataset))+ circle(hg19IdeogramCyto, geom = "ideo", fill = "gray70") + circle(hg19IdeogramCyto, geom = "scale", size = 2) + circle(hg19IdeogramCyto, geom = "text", aes(label = seqnames(hg19IdeogramCyto)), vjust = -1.5, size = 3)
However I get the error
Error in .local(data, ...) : label must be one of column names
This error doesn't appear if I revert to the previous version of ggplot2, keeping the same version of ggbio.
Any particular workaround?
I tried to put the names as metadata to the GRanges object and use the "column" name as label, but didn't help.
R version 3.4.2 (2017-09-28) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS High Sierra 10.13.4 Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/3.4/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] stats4 parallel tools grid stats graphics grDevices utils datasets methods base other attached packages: [1] BSgenome.Hsapiens.NCBI.GRCh38_1.3.1000 BiocInstaller_1.28.0 BSgenome_1.46.0 [4] rtracklayer_1.38.3 Biostrings_2.46.0 XVector_0.18.0 [7] GenomicRanges_1.30.3 GenomeInfoDb_1.14.0 IRanges_2.12.0 [10] S4Vectors_0.16.0 biomaRt_2.34.2 ggbio_1.26.1 [13] BiocGenerics_0.24.0 reshape_0.8.7 gplots_3.0.1 [16] bindrcpp_0.2.2 eulerr_4.1.0 GGally_1.4.0 [19] ggpmisc_0.3.0 VennDiagram_1.6.20 futile.logger_1.4.3 [22] pander_0.6.2 reshape2_1.4.3 forcats_0.3.0 [25] stringr_1.3.1 dplyr_0.7.6 purrr_0.2.5 [28] readr_1.1.1 tidyr_0.8.1 tibble_1.4.2 [31] ggplot2_3.0.0 tidyverse_1.2.1 knitr_1.20 loaded via a namespace (and not attached): [1] readxl_1.1.0 backports_1.1.2 Hmisc_4.1-1 AnnotationHub_2.10.1 [5] fastmatch_1.1-0 plyr_1.8.4 igraph_1.2.2 lazyeval_0.2.1 [9] splines_3.4.2 BiocParallel_1.12.0 digest_0.6.17 ensembldb_2.2.2 [13] htmltools_0.3.6 GOSemSim_2.4.1 GO.db_3.5.0 gdata_2.18.0 [17] fansi_0.3.0 magrittr_1.5 checkmate_1.8.5 memoise_1.1.0 [21] cluster_2.0.7-1 modelr_0.1.2 matrixStats_0.54.0 prettyunits_1.0.2 [25] colorspace_1.3-2 blob_1.1.1 rvest_0.3.2 haven_1.1.2 [29] crayon_1.3.4 RCurl_1.95-4.11 jsonlite_1.5 graph_1.56.0 [33] bindr_0.1.1 survival_2.42-6 VariantAnnotation_1.24.5 glue_1.3.0 [37] polyclip_1.9-1 gtable_0.2.0 zlibbioc_1.24.0 DelayedArray_0.4.1 [41] scales_1.0.0 DOSE_3.4.0 futile.options_1.0.1 DBI_1.0.0 [45] Rcpp_0.12.18 xtable_1.8-3 progress_1.2.0 htmlTable_1.12 [49] foreign_0.8-71 bit_1.1-14 OrganismDbi_1.20.0 Formula_1.2-3 [53] htmlwidgets_1.2 httr_1.3.1 fgsea_1.4.1 RColorBrewer_1.1-2 [57] acepack_1.4.1 pkgconfig_2.0.2 XML_3.98-1.16 nnet_7.3-12 [61] utf8_1.1.4 labeling_0.3 polynom_1.3-9 tidyselect_0.2.4 [65] rlang_0.2.2 later_0.7.5 AnnotationDbi_1.40.0 munsell_0.5.0 [69] cellranger_1.1.0 cli_1.0.0 RSQLite_2.1.1 broom_0.5.0 [73] evaluate_0.11 yaml_2.2.0 bit64_0.9-7 caTools_1.17.1.1 [77] AnnotationFilter_1.2.0 RBGL_1.54.0 nlme_3.1-137 mime_0.5 [81] formatR_1.5 DO.db_2.9 xml2_1.2.0 BiocStyle_2.6.1 [85] compiler_3.4.2 rstudioapi_0.7 curl_3.2 interactiveDisplayBase_1.16.0 [89] stringi_1.2.4 highr_0.7 GenomicFeatures_1.30.3 lattice_0.20-35 [93] ProtGenerics_1.10.0 Matrix_1.2-14 pillar_1.3.0 data.table_1.11.4 [97] bitops_1.0-6 httpuv_1.4.5 qvalue_2.10.0 R6_2.2.2 [101] latticeExtra_0.6-28 RMySQL_0.10.15 promises_1.0.1 KernSmooth_2.23-15 [105] gridExtra_2.3 lambda.r_1.2.3 dichromat_2.0-0 gtools_3.8.1 [109] assertthat_0.2.0 SummarizedExperiment_1.8.1 rprojroot_1.3-2 withr_2.1.2 [113] GenomicAlignments_1.14.2 Rsamtools_1.30.0 GenomeInfoDbData_1.0.0 hms_0.4.2 [117] clusterProfiler_3.6.0 rpart_4.1-13 rmarkdown_1.10 rvcheck_0.1.0 [121] biovizBase_1.26.0 Biobase_2.38.0 shiny_1.1.0 lubridate_1.7.4 [125] base64enc_0.1-3
Please update your R/Bioconductor and see if the problem persists. If it does, please let me know how you constructed "myGR".
Hi Michael,
I've updated also R to 3.5.1 now and it does work. and ggbio is now 1.28.5
the vignette is now updated to
instead of
might be useful for others to notice the change in the label, consistent with the message from ggplot.
no error now. thanks for the help!