aes label in ggbio_1.26.1 with ggplot2_3.0.0
Entering edit mode
Last seen 4.0 years ago

Hi guys,

I'm following the vignette to create a circular plot

  circle(myGR, geom = "link", = "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

[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             
ggbio ggplot2 • 555 views
Entering edit mode

Please update your R/Bioconductor and see if the problem persists. If it does, please let me know how you constructed "myGR".

Entering edit mode

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

circle(hg19sub, geom = "text", aes(label = seqnames), vjust = 0, size = 3)

instead of

circle(hg19sub, geom = "text", aes(label = seqnames(hg19sub)), vjust = -1.5, size = 3)

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!


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