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When using the DotPlot function in Seurat, the following warning is displayed:
DotPlot
lifecycle::last_lifecycle_warnings() [[1]] <warning/lifecycle_warning_deprecated> Warning: The `facets` argument of `facet_grid()` is deprecated as of ggplot2 2.2.0. ℹ Please use the `rows` argument instead. ℹ 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)")
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")
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
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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:Code example:
Session Info
The text was updated successfully, but these errors were encountered: