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Deprecated facets Argument Warning in DotPlot Function #9579

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ignagarlav opened this issue Dec 27, 2024 · 1 comment
Open

Deprecated facets Argument Warning in DotPlot Function #9579

ignagarlav opened this issue Dec 27, 2024 · 1 comment
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@ignagarlav
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Issue: Deprecated facets Argument in Seurat's DotPlot Function

When using the DotPlot function in Seurat, the following warning is displayed:

lifecycle::last_lifecycle_warnings()
[[1]]
<warning/lifecycle_warning_deprecated>
Warning:
The `facets` argument of `facet_grid()` is deprecated as of ggplot2 2.2.0.Please use the `rows` argument instead.The deprecated feature was likely used in the Seurat package.
  Please report the issue at <https://github.com/satijalab/seurat/issues>.
---
Backtrace:1. └─Seurat::DotPlot(obj, features = general_markers, group.by = "harmony.clusters")
 2.   └─ggplot2::facet_grid(...)
 3.     └─ggplot2:::deprecate_warn0("2.2.0", "facet_grid(facets)", "facet_grid(rows)")

Code example:

library(Seurat)
library(ggplot2)
set.seed(241224)

general_markers <- list(
  "Epithelial" = c("EPCAM","CDH1"),
  "Proliferating" = c("MKI67"))

DotPlot(obj, features = general_markers, group.by = "harmony.clusters") +
  theme(axis.text.x = element_text(angle = 45, hjust = 1),
        plot.title = element_text(size = 14, face = "bold", hjust = 0.5)
  ) +
  ggtitle(label = "TNBC")

Session Info

sessionInfo()
R version 4.4.1 (2024-06-14)
Platform: aarch64-apple-darwin20
Running under: macOS 15.1.1

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: Europe/Madrid
tzcode source: internal

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

other attached packages:
 [1] ggplot2_3.5.1         Seurat_5.0.0          SeuratObject_5.0.2   
 [4] sp_2.1-4              dplyr_1.1.4           biomaRt_2.60.1       
 [7] Matrix_1.7-1          GenomicRanges_1.56.2  GenomeInfoDb_1.40.1  
[10] IRanges_2.38.1        S4Vectors_0.42.1      BiocGenerics_0.50.0  
[13] anndata_0.7.5.6       convert2anndata_0.2.0 reticulate_1.40.0    

loaded via a namespace (and not attached):
  [1] RcppAnnoy_0.0.22            splines_4.4.1              
  [3] later_1.4.1                 filelock_1.0.3             
  [5] tibble_3.2.1                polyclip_1.10-7            
  [7] fastDummies_1.7.4           lifecycle_1.0.4            
  [9] httr2_1.0.7                 globals_0.16.3             
 [11] lattice_0.22-6              vroom_1.6.5                
 [13] MASS_7.3-61                 magrittr_2.0.3             
 [15] plotly_4.10.4               httpuv_1.6.15              
 [17] sctransform_0.4.1           spam_2.11-0                
 [19] spatstat.sparse_3.1-0       cowplot_1.1.3              
 [21] pbapply_1.7-2               DBI_1.2.3                  
 [23] RColorBrewer_1.1-3          pkgload_1.4.0              
 [25] abind_1.4-8                 zlibbioc_1.50.0            
 [27] Rtsne_0.17                  purrr_1.0.2                
 [29] rappdirs_0.3.3              GenomeInfoDbData_1.2.12    
 [31] ggrepel_0.9.6               irlba_2.3.5.1              
 [33] listenv_0.9.1               spatstat.utils_3.1-1       
 [35] goftest_1.2-3               RSpectra_0.16-2            
 [37] spatstat.random_3.3-2       fitdistrplus_1.2-1         
 [39] parallelly_1.40.1           leiden_0.4.3.1             
 [41] codetools_0.2-20            getopt_1.20.4              
 [43] DelayedArray_0.30.1         xml2_1.3.6                 
 [45] tidyselect_1.2.1            UCSC.utils_1.0.0           
 [47] farver_2.1.2                matrixStats_1.4.1          
 [49] BiocFileCache_2.12.0        spatstat.explore_3.3-3     
 [51] jsonlite_1.8.9              progressr_0.15.1           
 [53] ggridges_0.5.6              survival_3.7-0             
 [55] tools_4.4.1                 progress_1.2.3             
 [57] ica_1.0-3                   Rcpp_1.0.13-1              
 [59] glue_1.8.0                  gridExtra_2.3              
 [61] SparseArray_1.4.8           MatrixGenerics_1.16.0      
 [63] withr_3.0.2                 fastmap_1.2.0              
 [65] fansi_1.0.6                 digest_0.6.37              
 [67] R6_2.5.1                    mime_0.12                  
 [69] colorspace_2.1-1            scattermore_1.2            
 [71] tensor_1.5                  spatstat.data_3.1-4        
 [73] RSQLite_2.3.9               utf8_1.2.4                 
 [75] tidyr_1.3.1                 generics_0.1.3             
 [77] data.table_1.16.4           prettyunits_1.2.0          
 [79] httr_1.4.7                  htmlwidgets_1.6.4          
 [81] S4Arrays_1.4.1              uwot_0.2.2                 
 [83] pkgconfig_2.0.3             gtable_0.3.6               
 [85] blob_1.2.4                  lmtest_0.9-40              
 [87] SingleCellExperiment_1.26.0 XVector_0.44.0             
 [89] htmltools_0.5.8.1           dotCall64_1.2              
 [91] scales_1.3.0                Biobase_2.64.0             
 [93] png_0.1-8                   optparse_1.7.5             
 [95] spatstat.univar_3.1-1       rstudioapi_0.17.1          
 [97] tzdb_0.4.0                  reshape2_1.4.4             
 [99] nlme_3.1-166                curl_6.0.1                 
[101] zoo_1.8-12                  cachem_1.1.0               
[103] stringr_1.5.1               KernSmooth_2.23-24         
[105] parallel_4.4.1              miniUI_0.1.1.1             
[107] AnnotationDbi_1.66.0        pillar_1.9.0               
[109] grid_4.4.1                  vctrs_0.6.5                
[111] RANN_2.6.2                  promises_1.3.2             
[113] dbplyr_2.5.0                xtable_1.8-4               
[115] cluster_2.1.8               readr_2.1.5                
[117] cli_3.6.3                   compiler_4.4.1             
[119] rlang_1.1.4                 crayon_1.5.3               
[121] future.apply_1.11.3         labeling_0.4.3             
[123] plyr_1.8.9                  stringi_1.8.4              
[125] viridisLite_0.4.2           deldir_2.0-4               
[127] assertthat_0.2.1            munsell_0.5.1              
[129] Biostrings_2.72.1           lazyeval_0.2.2             
[131] spatstat.geom_3.3-4         RcppHNSW_0.6.0             
[133] hms_1.1.3                   patchwork_1.3.0            
[135] bit64_4.5.2                 future_1.34.0              
[137] KEGGREST_1.44.1             shiny_1.10.0               
[139] SummarizedExperiment_1.34.0 ROCR_1.0-11                
[141] igraph_2.1.2                memoise_2.0.1              
[143] bit_4.5.0.1      
@ignagarlav ignagarlav added the bug Something isn't working label Dec 27, 2024
@rharao
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rharao commented Dec 27, 2024

Thanks for reporting this. A fix has been submitted at #9409 and is awaiting review by the development team.

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