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plot_density not working

Open ftencaten opened this issue 4 months ago • 15 comments

I've used plot_density several times but today I ran into this error and couldn't find more details about it. Is it possible related to the recent Seurat update?

library(Nebulosa) Loading required package: ggplot2 Loading required package: patchwork data <- SeuratObject::pbmc_small plot_density(data,"CD3E") Error in as.vector(x, "character") : cannot coerce type 'environment' to vector of type 'character' sessionInfo() R version 4.3.2 (2023-10-31) Platform: x86_64-apple-darwin20 (64-bit) Running under: macOS Sonoma 14.3.1

Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0

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: America/New_York tzcode source: internal

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

other attached packages: [1] Nebulosa_1.12.0 patchwork_1.2.0 ggplot2_3.5.0

loaded via a namespace (and not attached): [1] RColorBrewer_1.1-3 rstudioapi_0.15.0 jsonlite_1.8.8
[4] magrittr_2.0.3 spatstat.utils_3.0-4 farver_2.1.1
[7] zlibbioc_1.48.0 vctrs_0.6.5 ROCR_1.0-11
[10] spatstat.explore_3.2-6 RCurl_1.98-1.14 S4Arrays_1.2.0
[13] htmltools_0.5.7 SparseArray_1.2.3 pracma_2.4.4
[16] sctransform_0.4.1 parallelly_1.37.0 KernSmooth_2.23-22
[19] htmlwidgets_1.6.4 ica_1.0-3 plyr_1.8.9
[22] plotly_4.10.4 zoo_1.8-12 igraph_2.0.2
[25] mime_0.12 lifecycle_1.0.4 pkgconfig_2.0.3
[28] Matrix_1.6-5 R6_2.5.1 fastmap_1.1.1
[31] GenomeInfoDbData_1.2.11 MatrixGenerics_1.14.0 fitdistrplus_1.1-11
[34] future_1.33.1 shiny_1.8.0 digest_0.6.34
[37] colorspace_2.1-0 S4Vectors_0.40.2 Seurat_5.0.1
[40] tensor_1.5 RSpectra_0.16-1 irlba_2.3.5.1
[43] GenomicRanges_1.54.1 labeling_0.4.3 progressr_0.14.0
[46] fansi_1.0.6 spatstat.sparse_3.0-3 httr_1.4.7
[49] polyclip_1.10-6 abind_1.4-5 compiler_4.3.2
[52] withr_3.0.0 fastDummies_1.7.3 MASS_7.3-60.0.1
[55] DelayedArray_0.28.0 tools_4.3.2 lmtest_0.9-40
[58] httpuv_1.6.14 future.apply_1.11.1 goftest_1.2-3
[61] glue_1.7.0 nlme_3.1-164 promises_1.2.1
[64] grid_4.3.2 Rtsne_0.17 cluster_2.1.6
[67] reshape2_1.4.4 generics_0.1.3 gtable_0.3.4
[70] spatstat.data_3.0-4 tidyr_1.3.1 data.table_1.15.0
[73] sp_2.1-3 utf8_1.2.4 XVector_0.42.0
[76] BiocGenerics_0.48.1 spatstat.geom_3.2-8 RcppAnnoy_0.0.22
[79] ggrepel_0.9.5 RANN_2.6.1 pillar_1.9.0
[82] stringr_1.5.1 spam_2.10-0 RcppHNSW_0.6.0
[85] later_1.3.2 splines_4.3.2 dplyr_1.1.4
[88] lattice_0.22-5 survival_3.5-8 deldir_2.0-2
[91] ks_1.14.2 tidyselect_1.2.0 SingleCellExperiment_1.24.0 [94] miniUI_0.1.1.1 pbapply_1.7-2 gridExtra_2.3
[97] IRanges_2.36.0 SummarizedExperiment_1.32.0 scattermore_1.2
[100] stats4_4.3.2 Biobase_2.62.0 matrixStats_1.2.0
[103] stringi_1.8.3 lazyeval_0.2.2 codetools_0.2-19
[106] tibble_3.2.1 cli_3.6.2 uwot_0.1.16
[109] xtable_1.8-4 reticulate_1.35.0 munsell_0.5.0
[112] Rcpp_1.0.12 GenomeInfoDb_1.38.5 globals_0.16.2
[115] spatstat.random_3.2-2 png_0.1-8 parallel_4.3.2
[118] ellipsis_0.3.2 mclust_6.1 dotCall64_1.1-1
[121] bitops_1.0-7 listenv_0.9.1 mvtnorm_1.2-4
[124] viridisLite_0.4.2 scales_1.3.0 ggridges_0.5.6
[127] crayon_1.5.2 SeuratObject_5.0.1 leiden_0.4.3.1
[130] purrr_1.0.2 rlang_1.1.3 cowplot_1.1.3

ftencaten avatar Feb 27 '24 02:02 ftencaten