yulab-smu/ggsc

🧠 Visualizing Single Cell and Spatial Transcriptomics

ggsc's Issues

The "mapping" parameter cannot be used correctly when using sc_dim()

My code:

> sc_dim(sce.all.int, reduction = "tsne", mapping = aes(colour = RNA_snn_res.0.8))
Error:
! Problem while computing aesthetics.
ℹ Error occurred in the 1st layer.
Caused by error:
! object 'RNA_snn_res.0.8' not found
Run `rlang::last_trace()` to see where the error occurred.
> rlang::last_trace()
<error/rlang_error>
Error:
! Problem while computing aesthetics.
ℹ Error occurred in the 1st layer.
Caused by error:
! object 'RNA_snn_res.0.8' not found
---
Backtrace:
     ▆
  1. ├─base (local) `<fn>`(x)
  2. └─ggplot2:::print.ggplot(x)
  3.   ├─ggplot2::ggplot_build(x)
  4.   └─ggplot2:::ggplot_build.ggplot(x)
  5.     └─ggplot2:::by_layer(...)
  6.       ├─rlang::try_fetch(...)
  7.       │ ├─base::tryCatch(...)
  8.       │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
  9.       │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 10.       │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
 11.       │ └─base::withCallingHandlers(...)
 12.       └─ggplot2 (local) f(l = layers[[i]], d = data[[i]])
 13.         └─l$compute_aesthetics(d, plot)
 14.           └─ggplot2 (local) compute_aesthetics(..., self = self)
 15.             └─ggplot2:::scales_add_defaults(...)
 16.               └─base::lapply(aesthetics[new_aesthetics], eval_tidy, data = data)
 17.                 └─rlang (local) FUN(X[[i]], ...)
Run rlang::last_trace(drop = FALSE) to see 5 hidden frames.
> rlang::last_trace(drop = FALSE)
<error/rlang_error>
Error:
! Problem while computing aesthetics.
ℹ Error occurred in the 1st layer.
Caused by error:
! object 'RNA_snn_res.0.8' not found
---
Backtrace:
     ▆
  1. ├─base (local) `<fn>`(x)
  2. ├─ggplot2:::print.ggplot(x)
  3. │ ├─ggplot2::ggplot_build(x)
  4. │ └─ggplot2:::ggplot_build.ggplot(x)
  5. │   └─ggplot2:::by_layer(...)
  6. │     ├─rlang::try_fetch(...)
  7. │     │ ├─base::tryCatch(...)
  8. │     │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
  9. │     │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 10. │     │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
 11. │     │ └─base::withCallingHandlers(...)
 12. │     └─ggplot2 (local) f(l = layers[[i]], d = data[[i]])
 13. │       └─l$compute_aesthetics(d, plot)
 14. │         └─ggplot2 (local) compute_aesthetics(..., self = self)
 15. │           └─ggplot2:::scales_add_defaults(...)
 16. │             └─base::lapply(aesthetics[new_aesthetics], eval_tidy, data = data)
 17. │               └─rlang (local) FUN(X[[i]], ...)
 18. └─base::.handleSimpleError(...)
 19.   └─rlang (local) h(simpleError(msg, call))
 20.     └─handlers[[1L]](cnd)
 21.       └─cli::cli_abort(...)
 22.         └─rlang::abort(...)

It seems that the specified column could not be found in the seurat object.

> colnames([e-mail])
 [1] "orig.ident"       "nCount_RNA"       "nFeature_RNA"     "percent_mito"     "percent_ribo"     "percent_hb"       "RNA_snn_res.0.01"
 [8] "seurat_clusters"  "RNA_snn_res.0.05" "RNA_snn_res.0.1"  "RNA_snn_res.0.2"  "RNA_snn_res.0.3"  "RNA_snn_res.0.5"  "RNA_snn_res.0.8" 
[15] "RNA_snn_res.1" 

sessionInfo:

> sessionInfo()
R version 4.3.1 (2023-06-16)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04.3 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0 
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0

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       

time zone: Asia/Shanghai
tzcode source: system (glibc)

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

other attached packages:
 [1] ggsc_1.0.2         patchwork_1.1.3    cowplot_1.1.1      clustree_0.5.1     ggraph_2.1.0       future_1.33.0      lubridate_1.9.3   
 [8] forcats_1.0.0      stringr_1.5.1      dplyr_1.1.4        purrr_1.0.2        readr_2.1.4        tidyr_1.3.0        tibble_3.2.1      
[15] tidyverse_2.0.0    ggsci_3.0.0        harmony_1.1.0      Rcpp_1.0.11        COSG_0.9.0         R.utils_2.12.3     R.oo_1.25.0       
[22] R.methodsS3_1.8.2  data.table_1.14.8  ggplot2_3.4.4      SeuratObject_4.1.3 Seurat_4.3.0       Matrix_1.6-1.1    

loaded via a namespace (and not attached):
  [1] RcppAnnoy_0.0.21            splines_4.3.1               later_1.3.1                 bitops_1.0-7               
  [5] polyclip_1.10-6             lifecycle_1.0.4             globals_0.16.2              lattice_0.22-5             
  [9] MASS_7.3-60                 magrittr_2.0.3              plotly_4.10.3               httpuv_1.6.12              
 [13] sctransform_0.4.1           spam_2.10-0                 sp_2.1-1                    spatstat.sparse_3.0-3      
 [17] reticulate_1.34.0           pbapply_1.7-2               RColorBrewer_1.1-3          abind_1.4-5                
 [21] zlibbioc_1.48.0             Rtsne_0.16                  GenomicRanges_1.54.1        BiocGenerics_0.48.1        
 [25] RCurl_1.98-1.13             yulab.utils_0.1.0           tweenr_2.0.2                GenomeInfoDbData_1.2.11    
 [29] IRanges_2.36.0              S4Vectors_0.40.2            ggrepel_0.9.4               irlba_2.3.5.1              
 [33] listenv_0.9.0               spatstat.utils_3.0-4        goftest_1.2-3               spatstat.random_3.2-1      
 [37] fitdistrplus_1.1-11         parallelly_1.36.0           leiden_0.4.3.1              codetools_0.2-19           
 [41] DelayedArray_0.28.0         ggforce_0.4.1               tidyselect_1.2.0            farver_2.1.1               
 [45] viridis_0.6.4               matrixStats_1.1.0           stats4_4.3.1                spatstat.explore_3.2-5     
 [49] jsonlite_1.8.7              ellipsis_0.3.2              tidygraph_1.2.3             progressr_0.14.0           
 [53] ggridges_0.5.4              survival_3.5-7              tools_4.3.1                 ica_1.0-3                  
 [57] glue_1.6.2                  gridExtra_2.3               SparseArray_1.2.2           MatrixGenerics_1.14.0      
 [61] GenomeInfoDb_1.38.1         withr_2.5.2                 fastmap_1.1.1               fansi_1.0.5                
 [65] digest_0.6.33               timechange_0.2.0            R6_2.5.1                    mime_0.12                  
 [69] colorspace_2.1-0            scattermore_1.2             tensor_1.5                  spatstat.data_3.0-3        
 [73] utf8_1.2.4                  generics_0.1.3              graphlayouts_1.0.2          httr_1.4.7                 
 [77] htmlwidgets_1.6.3           S4Arrays_1.2.0              uwot_0.1.16                 pkgconfig_2.0.3            
 [81] gtable_0.3.4                lmtest_0.9-40               SingleCellExperiment_1.24.0 XVector_0.42.0             
 [85] shadowtext_0.1.2            htmltools_0.5.7             dotCall64_1.1-1             scales_1.3.0               
 [89] Biobase_2.62.0              png_0.1-8                   ggfun_0.1.3                 rstudioapi_0.15.0          
 [93] tzdb_0.4.0                  reshape2_1.4.4              nlme_3.1-164                cachem_1.0.8               
 [97] zoo_1.8-12                  KernSmooth_2.23-22          parallel_4.3.1              miniUI_0.1.1.1             
[101] pillar_1.9.0                grid_4.3.1                  vctrs_0.6.4                 RANN_2.6.1                 
[105] promises_1.2.1              tidydr_0.0.5                xtable_1.8-4                cluster_2.1.6              
[109] cli_3.6.1                   compiler_4.3.1              rlang_1.1.2                 crayon_1.5.2               
[113] future.apply_1.11.0         labeling_0.4.3              fs_1.6.3                    plyr_1.8.9                 
[117] stringi_1.8.2               viridisLite_0.4.2           deldir_2.0-2                munsell_0.5.0              
[121] lazyeval_0.2.2              spatstat.geom_3.2-7         hms_1.1.3                   shiny_1.8.0                
[125] SummarizedExperiment_1.32.0 ROCR_1.0-11                 memoise_2.0.1               igraph_1.5.1               
[129] RcppParallel_5.1.7