plot_measure_dim error

[WesAus10]

Hi, I recently found your package and love it but I ran into an error when trying to call plot_measure_dim. Example below uses the tutorial data.

> plot_measure_dim(dataset = scRNA_int, 
+          measures = c("nFeature_RNA","nCount_RNA","percent.mt","KRT14"))
Error in `plot_measure_dim()`:
! Can't subset `.data` outside of a data mask context.
Run `rlang::last_error()` to see where the error occurred.
> rlang::last_error()
<error/rlang_error>
Error in `plot_measure_dim()`:
! Can't subset `.data` outside of a data mask context.
---
Backtrace:
 1. Scillus::plot_measure_dim(...)
Run `rlang::last_trace()` to see the full context.
> rlang::last_trace()
<error/rlang_error>
Error in `plot_measure_dim()`:
! Can't subset `.data` outside of a data mask context.
---
Backtrace:
    ▆
 1. └─**Scillus**::plot_measure_dim(...)
 2.   ├─ggplot2::scale_color_viridis_c(...)
 3.   │ └─ggplot2::continuous_scale(...)
 4.   ├─**stats**::quantile(.data[[measures[i]]], probs = 0.1)
 5.   ├─<unknown>
 6.   └─**rlang**:::`[[.rlang_fake_data_pronoun`(.data, measures[i])
 7.     └─rlang:::stop_fake_data_subset(call)
 8.       └─rlang::abort(...)

Here's my sessionInfo

> sessionInfo()
R version 4.1.3 (2022-03-10)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Monterey 12.3

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/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] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] magrittr_2.0.3     SeuratObject_4.0.4 Seurat_4.1.0       forcats_0.5.1     
 [5] stringr_1.4.0      dplyr_1.0.8        purrr_0.3.4        readr_2.1.2       
 [9] tidyr_1.2.0        tibble_3.1.6       ggplot2_3.3.5      tidyverse_1.3.1   
[13] Scillus_0.5.0     

loaded via a namespace (and not attached):
  [1] readxl_1.4.0          backports_1.4.1       circlize_0.4.14      
  [4] plyr_1.8.7            igraph_1.3.0          lazyeval_0.2.2       
  [7] splines_4.1.3         listenv_0.8.0         scattermore_0.8      
 [10] digest_0.6.29         foreach_1.5.2         htmltools_0.5.2      
 [13] formattable_0.2.1     fansi_1.0.3           tensor_1.5           
 [16] cluster_2.1.3         doParallel_1.0.17     ROCR_1.0-11          
 [19] tzdb_0.3.0            ComplexHeatmap_2.10.0 globals_0.14.0       
 [22] modelr_0.1.8          matrixStats_0.61.0    R.utils_2.11.0       
 [25] spatstat.sparse_2.1-0 colorspace_2.0-3      rvest_1.0.2          
 [28] ggrepel_0.9.1         haven_2.4.3           xfun_0.30            
 [31] crayon_1.5.1          jsonlite_1.8.0        spatstat.data_2.1-4  
 [34] survival_3.3-1        zoo_1.8-9             iterators_1.0.14     
 [37] glue_1.6.2            polyclip_1.10-0       gtable_0.3.0         
 [40] leiden_0.3.9          GetoptLong_1.0.5      future.apply_1.8.1   
 [43] shape_1.4.6           BiocGenerics_0.40.0   abind_1.4-5          
 [46] scales_1.1.1          DBI_1.1.2             spatstat.random_2.2-0
 [49] miniUI_0.1.1.1        Rcpp_1.0.8.3          viridisLite_0.4.0    
 [52] xtable_1.8-4          clue_0.3-60           reticulate_1.24      
 [55] spatstat.core_2.4-2   stats4_4.1.3          htmlwidgets_1.5.4    
 [58] httr_1.4.2            RColorBrewer_1.1-3    ellipsis_0.3.2       
 [61] ica_1.0-2             farver_2.1.0          R.methodsS3_1.8.1    
 [64] pkgconfig_2.0.3       uwot_0.1.11           dbplyr_2.1.1         
 [67] deldir_1.0-6          utf8_1.2.2            labeling_0.4.2       
 [70] tidyselect_1.1.2      rlang_1.0.2           reshape2_1.4.4       
 [73] later_1.3.0           cellranger_1.1.0      munsell_0.5.0        
 [76] tools_4.1.3           cli_3.2.0             generics_0.1.2       
 [79] broom_0.8.0           ggridges_0.5.3        evaluate_0.15        
 [82] fastmap_1.1.0         goftest_1.2-3         fs_1.5.2             
 [85] knitr_1.38            fitdistrplus_1.1-8    RANN_2.6.1           
 [88] pbapply_1.5-0         future_1.24.0         nlme_3.1-157         
 [91] mime_0.12             R.oo_1.24.0           xml2_1.3.3           
 [94] rstudioapi_0.13       compiler_4.1.3        plotly_4.10.0        
 [97] png_0.1-7             spatstat.utils_2.3-0  reprex_2.0.1         
[100] stringi_1.7.6         RSpectra_0.16-0       lattice_0.20-45      
[103] Matrix_1.4-1          vctrs_0.4.1           pillar_1.7.0         
[106] lifecycle_1.0.1       spatstat.geom_2.4-0   lmtest_0.9-40        
[109] GlobalOptions_0.1.2   RcppAnnoy_0.0.19      data.table_1.14.2    
[112] cowplot_1.1.1         irlba_2.3.5           httpuv_1.6.5         
[115] patchwork_1.1.1       R6_2.5.1              promises_1.2.0.1     
[118] KernSmooth_2.23-20    gridExtra_2.3         IRanges_2.28.0       
[121] parallelly_1.31.0     codetools_0.2-18      MASS_7.3-56          
[124] assertthat_0.2.1      rjson_0.2.21          withr_2.5.0          
[127] sctransform_0.3.3     S4Vectors_0.32.4      mgcv_1.8-40          
[130] parallel_4.1.3        hms_1.1.1             grid_4.1.3           
[133] rpart_4.1.16          rmarkdown_2.13        Rtsne_0.15           
[136] shiny_1.7.1           lubridate_1.8.0

[yaqi2731]

The same mistake!

[yaqi2731]

Excuse me, has this problem been solved? Is there any technician who can help to solve it?

[NCtraveling]

ISSUE SOLVED @WesAus10 @yaqi2731

I got this error too. I tried to change every .data to df in the source code of the function plot_measure_dim()

Fortunately, it works!!! But I don't understand why...

You could build a new function (e.g. plot_measure_dim2) by yourselves:

plot_measure_dim2 <- function (dataset, measures, split_by = NA, point.size = 1) 
  {
    l <- get_measure_data(dataset = dataset, measures = measures, 
                          return_df = FALSE)
    split_by <- ifelse(split_by == "No Split", NA, split_by)
    df <- l[[1]]
    measures <- l[[2]]
    p <- list()
    for (i in seq_along(1:length(measures))) {
      p[[i]] <- ggplot(df) + geom_point(aes(x = UMAP_1, 
                                            y = UMAP_2, color = df[[measures[i]]]), 
                                        size = point.size) + scale_color_viridis_c(option = "A", 
                                                                                   name = "", direction = -1, limits = c(quantile(df[[measures[i]]], 
                                                                                                                                  probs = 0.1), quantile(df[[measures[i]]], 
                                                                                                                                                         probs = 0.9)), oob = scales::squish) + theme(panel.grid.major = element_blank(), 
                                                                                                                                                                                                      panel.grid.minor = element_blank(), panel.background = element_blank(), 
                                                                                                                                                                                                      axis.text = element_text(size = 12), axis.title = element_text(size = 12), 
                                                                                                                                                                                                      panel.border = element_rect(colour = "black", fill = NA, 
                                                                                                                                                                                                                                  linewidth = 1, linetype = 1), axis.line = element_blank()) + 
        labs(x = "UMAP_1", y = "UMAP_2") + ggtitle(measures[i]) + 
        if (!is.na(split_by)) {
          facet_wrap(as.formula(paste("~", split_by)))
        }
      else {
        theme(aspect.ratio = 1)
      }
    }
    patchwork::wrap_plots(p)
  }