sc.plot2dWithMargins Error

[moshl]

Hi,the func "sc.plot2dWithMargins " was okay before, but now, it always report the error as below,
Error: $ operator is invalid for atomic vectors
hope you reply. Many thanks.
Mo

[chrisamiller]

I'd need to see some example code and data that I can use to reproduce the problem. Provide that, and I'll be happy to take a look. Also, pasting the output of sessionInfo() would be helpful!

[Ninomoriaty]

I meet the same problem when running run.R in manuscript/data/figure3 with data provided by https://github.com/genome/sciclone-meta and here is the output of my sessionInfo() result.

R version 3.6.1 (2019-07-05)
Platform: x86_64-conda_cos6-linux-gnu (64-bit)
Running under: Ubuntu 18.04.3 LTS

Matrix products: default
BLAS/LAPACK: /home/ninomoriaty/anaconda3/envs/EvolCancer/lib/R/lib/libRblas.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=zh_CN.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=zh_CN.UTF-8    LC_MESSAGES=en_US.UTF-8    LC_PAPER=zh_CN.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=zh_CN.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
 [1] grid      stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] sciClone_1.1.0      TeachingDemos_2.10  MKmisc_1.6          plotrix_3.7-6       RColorBrewer_1.1-2  rgl_0.100.30       
 [7] bmm_0.3.1           NORMT3_1.0-3        ggplot2_3.2.1       IRanges_2.18.3      S4Vectors_0.22.1    BiocGenerics_0.30.0

loaded via a namespace (and not attached):
  [1] tidyselect_0.2.5                  RSQLite_2.1.2                     AnnotationDbi_1.46.1             
  [4] htmlwidgets_1.5.1                 BiocParallel_1.18.1               pdp_0.7.0                        
  [7] devtools_2.2.1                    munsell_0.5.0                     miniUI_0.1.1.1                   
 [10] withr_2.1.2                       colorspace_1.4-1                  GOSemSim_2.10.0                  
 [13] Biobase_2.44.0                    knitr_1.25                        rstudioapi_0.10                  
 [16] robustbase_0.93-5                 DOSE_3.10.2                       labeling_0.3                     
 [19] urltools_1.7.3                    GenomeInfoDbData_1.2.1            polyclip_1.10-0                  
 [22] bit64_0.9-7                       farver_1.1.0                      rprojroot_1.3-2                  
 [25] vctrs_0.2.0                       xfun_0.10                         timescape_1.8.0                  
 [28] R6_2.4.0                          GenomeInfoDb_1.20.0               graphlayouts_0.5.0               
 [31] manipulateWidget_0.10.0           bitops_1.0-6                      fgsea_1.10.1                     
 [34] gridGraphics_0.4-1                DelayedArray_0.10.0               assertthat_0.2.1                 
 [37] promises_1.1.0                    scales_1.0.0                      ggraph_2.0.0                     
 [40] enrichplot_1.4.0                  gtable_0.3.0                      processx_3.4.1                   
 [43] tidygraph_1.1.2                   rlang_0.4.1                       zeallot_0.1.0                    
 [46] splines_3.6.1                     rtracklayer_1.44.4                lazyeval_0.2.2                   
 [49] europepmc_0.3                     checkmate_1.9.4                   BiocManager_1.30.9               
 [52] reshape2_1.4.3                    crosstalk_1.0.0                   backports_1.1.5                  
 [55] httpuv_1.5.2                      Meskit_0.1.0                      qvalue_2.16.0                    
 [58] clusterProfiler_3.12.0            tools_3.6.1                       usethis_1.5.1                    
 [61] ggplotify_0.0.4                   ellipsis_0.3.0                    sessioninfo_1.1.1                
 [64] ggridges_0.5.1                    Rcpp_1.0.2                        plyr_1.8.4                       
 [67] progress_1.2.2                    zlibbioc_1.30.0                   purrr_0.3.3                      
 [70] RCurl_1.95-4.12                   ps_1.3.0                          prettyunits_1.0.2                
 [73] viridis_0.5.1                     cowplot_1.0.0                     SummarizedExperiment_1.14.1      
 [76] ggrepel_0.8.1                     fs_1.3.1                          magrittr_1.5                     
 [79] data.table_1.12.6                 DO.db_2.9                         triebeard_0.3.0                  
 [82] reactome.db_1.68.0                matrixStats_0.55.0                pkgload_1.0.2                    
 [85] hms_0.5.1                         mime_0.7                          xtable_1.8-4                     
 [88] XML_3.98-1.20                     gridExtra_2.3                     testthat_2.2.1                   
 [91] compiler_3.6.1                    tibble_2.1.3                      crayon_1.3.4                     
 [94] BSgenome.Hsapiens.UCSC.hg19_1.4.0 htmltools_0.4.0                   later_1.0.0                      
 [97] tidyr_1.0.0                       ReactomePA_1.28.0                 DBI_1.0.0                        
[100] tweenr_1.0.1                      corrplot_0.84                     MASS_7.3-51.4                    
[103] rappdirs_0.3.1                    Matrix_1.2-17                     cli_1.1.0                        
[106] igraph_1.2.4.1                    GenomicRanges_1.36.1              pkgconfig_2.0.3                  
[109] rvcheck_0.1.5                     GenomicAlignments_1.20.1          xml2_1.2.2                       
[112] webshot_0.5.1                     XVector_0.24.0                    clonevol_0.99.11                 
[115] stringr_1.4.0                     callr_3.3.2                       digest_0.6.22                    
[118] graph_1.62.0                      Biostrings_2.52.0                 fastmatch_1.1-0                  
[121] curl_4.2                          shiny_1.4.0                       Rsamtools_2.0.3                  
[124] graphite_1.30.0                   lifecycle_0.1.0                   nlme_3.1-141                     
[127] jsonlite_1.6                      desc_1.2.0                        viridisLite_0.3.0                
[130] limma_3.40.6                      BSgenome_1.52.0                   pillar_1.4.2                     
[133] ggsci_2.9                         lattice_0.20-38                   deconstructSigs_1.8.0            
[136] fastmap_1.0.1                     httr_1.4.1                        DEoptimR_1.0-8                   
[139] pkgbuild_1.0.6                    GO.db_3.8.2                       glue_1.3.1                       
[142] remotes_2.1.0                     UpSetR_1.4.0                      fishplot_0.5                     
[145] bit_1.1-14                        ggforce_0.3.1                     stringi_1.4.3                    
[148] blob_1.2.0                        memoise_1.1.0                     dplyr_0.8.3                      
[151] ape_5.3  

Thank you for your attention and we will be grateful for your reply.

Wang Chengwei

[Ninomoriaty]

After simply testing, I found that this line in function sc.plot2dWithMargins may cause the problem:

max.density <- max(tmp[["data"]][[1]]$ymax)

As the variable ymax is set to be NULL and tmp[["data"]][[1]] seems to be a vector, it may lead to the error:

Error: $ operator is invalid for atomic vectors

However, I meet another problem caused by downViewport('panel.3-4-3-4') and the error is :

Error in grid.Call.graphics(C_downviewport, name$name, strict) : 
  Viewport 'panel.3-4-3-4' was not found

This error confuses me as it seems that panel.3-4-3-4 appears only once and I don't know how to check it. I would be really thankful if there are any technical solutions provided.

Wang Chengwei