Closed denvercal1234GitHub closed 11 months ago
Hi there,
I was trying to follow this tutorial (https://stemangiola.github.io/tidyseurat/), but I encountered the error "Error: 'ggplot' is not an exported object from 'namespace:tidyseurat'".
Would you mind advising me how to proceed?
Thank you.
> sessionInfo() R version 4.3.1 (2023-06-16) Platform: aarch64-apple-darwin20 (64-bit) Running under: macOS Sonoma 14.1.1 Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/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: Europe/London tzcode source: internal attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] ggplot2_3.4.4 tidyr_1.3.0 dplyr_1.1.4 tidyseurat_0.7.8 ttservice_0.4.0 reticulate_1.34.0 knitr_1.45 [8] SeuratObject_5.0.1 sp_2.1-1 loaded via a namespace (and not attached): [1] RColorBrewer_1.1-3 rstudioapi_0.15.0 jsonlite_1.8.7 magrittr_2.0.3 spatstat.utils_3.0-4 [6] fs_1.6.3 vctrs_0.6.4 ROCR_1.0-11 spatstat.explore_3.2-5 memoise_2.0.1 [11] rstatix_0.7.2 htmltools_0.5.7 usethis_2.2.2 curl_5.1.0 broom_1.0.5 [16] sctransform_0.4.1 parallelly_1.36.0 KernSmooth_2.23-22 htmlwidgets_1.6.2 ica_1.0-3 [21] plyr_1.8.9 plotly_4.10.3 zoo_1.8-12 cachem_1.0.8 igraph_1.5.1 [26] mime_0.12 lifecycle_1.0.4 pkgconfig_2.0.3 Matrix_1.6-3 R6_2.5.1 [31] fastmap_1.1.1 fitdistrplus_1.1-11 future_1.33.0 shiny_1.8.0 digest_0.6.33 [36] colorspace_2.1-0 patchwork_1.1.3 ps_1.7.5 tensor_1.5 Seurat_5.0.1 [41] RSpectra_0.16-1 irlba_2.3.5.1 pkgload_1.3.3 ggpubr_0.6.0 progressr_0.14.0 [46] spatstat.sparse_3.0-3 fansi_1.0.5 polyclip_1.10-6 httr_1.4.7 abind_1.4-5 [51] compiler_4.3.1 remotes_2.4.2.1 withr_2.5.2 backports_1.4.1 carData_3.0-5 [56] fastDummies_1.7.3 pkgbuild_1.4.2 ggsignif_0.6.4 MASS_7.3-60 sessioninfo_1.2.2 [61] tools_4.3.1 lmtest_0.9-40 httpuv_1.6.12 future.apply_1.11.0 goftest_1.2-3 [66] glue_1.6.2 callr_3.7.3 nlme_3.1-163 promises_1.2.1 grid_4.3.1 [71] Rtsne_0.16 cluster_2.1.4 reshape2_1.4.4 generics_0.1.3 spatstat.data_3.0-3 [76] gtable_0.3.4 data.table_1.14.8 car_3.1-2 utf8_1.2.4 spatstat.geom_3.2-7 [81] RcppAnnoy_0.0.21 ggrepel_0.9.4 RANN_2.6.1 pillar_1.9.0 stringr_1.5.1 [86] spam_2.10-0 RcppHNSW_0.5.0 later_1.3.1 splines_4.3.1 lattice_0.22-5 [91] deldir_1.0-9 survival_3.5-7 tidyselect_1.2.0 miniUI_0.1.1.1 pbapply_1.7-2 [96] randomcoloR_1.1.0.1 gridExtra_2.3 V8_4.4.0 scattermore_1.2 xfun_0.41 [101] devtools_2.4.5 matrixStats_1.1.0 stringi_1.8.1 lazyeval_0.2.2 codetools_0.2-19 [106] tibble_3.2.1 BiocManager_1.30.22 cli_3.6.1 uwot_0.1.16 xtable_1.8-4 [111] munsell_0.5.0 processx_3.8.2 Rcpp_1.0.11 spatstat.random_3.2-1 globals_0.16.2 [116] png_0.1-8 parallel_4.3.1 ellipsis_0.3.2 prettyunits_1.2.0 dotCall64_1.1-0 [121] profvis_0.3.8 urlchecker_1.0.1 listenv_0.9.0 viridisLite_0.4.2 scales_1.2.1 [126] ggridges_0.5.4 leiden_0.4.3.1 purrr_1.0.2 crayon_1.5.2 rlang_1.1.2 [131] cowplot_1.1.1
Solved by restarting and reinstalling.
Now you don't need to do tidyseurat::ggplot anymore, Just ggplot. I will fix the vignette.
tidyseurat::ggplot
ggplot
Hi there,
I was trying to follow this tutorial (https://stemangiola.github.io/tidyseurat/), but I encountered the error "Error: 'ggplot' is not an exported object from 'namespace:tidyseurat'".
Would you mind advising me how to proceed?
Thank you.