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Question: aes label in ggbio_1.26.1 with ggplot2_3.0.0
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gravatar for Lescai, Francesco
12 weeks ago by
Denmark
Lescai, Francesco380 wrote:

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             
ADD COMMENTlink written 12 weeks ago by Lescai, Francesco380
1

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

ADD REPLYlink written 12 weeks ago by Michael Lawrence10k

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!

ADD REPLYlink written 12 weeks ago by Lescai, Francesco380
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