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Bug in compare_group_interactions

Open UboCA opened this issue 2 years ago • 1 comments

Hi celltalkerTeam When I tried to run demo in different released version of celltalker, I'm stuck in the same site as follows.

> group_stats <- compare_group_interactions(seurat_object=ser_obj,
+   interaction_stats=top_stats_tonsil,
+   sample_replicates="sample_id",
+   sample_groups="sample_type",
+   metadata_grouping="cell_types")
Error in `dplyr::select()`:
! <text>:1:5: unexpected symbol
1: Use of
        ^
Backtrace:
 1. celltalker::compare_group_interactions(...)
 6. dplyr:::select.data.frame(...)

And I checked the function compare_group_interactions but just no cule.

R version 4.2.1 (2022-06-23)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.4 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8   
 [6] LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] magrittr_2.0.3        dplyr_1.0.10          sp_1.5-0              SeuratObject_4.1.2    Seurat_4.2.0          celltalker_0.0.6.9000

loaded via a namespace (and not attached):
  [1] Rtsne_0.16            colorspace_2.0-3      deldir_1.0-6          ellipsis_0.3.2        ggridges_0.5.4        rprojroot_2.0.3       circlize_0.4.15      
  [8] GlobalOptions_0.1.2   fs_1.5.2              spatstat.data_3.0-0   rstudioapi_0.14       farver_2.1.1          leiden_0.4.3          listenv_0.8.0        
 [15] remotes_2.4.2         ggrepel_0.9.1         fansi_1.0.3           codetools_0.2-18      splines_4.2.1         cachem_1.0.6          knitr_1.40           
 [22] polyclip_1.10-4       pkgload_1.3.0         jsonlite_1.8.3        ica_1.0-3             cluster_2.1.3         png_0.1-7             rgeos_0.5-9          
 [29] uwot_0.1.14           spatstat.sparse_3.0-0 shiny_1.7.2           sctransform_0.3.5     compiler_4.2.1        httr_1.4.4            assertthat_0.2.1     
 [36] Matrix_1.5-1          fastmap_1.1.0         lazyeval_0.2.2        cli_3.4.1             later_1.3.0           htmltools_0.5.3       prettyunits_1.1.1    
 [43] tools_4.2.1           igraph_1.3.5          gtable_0.3.1          glue_1.6.2            RANN_2.6.1            reshape2_1.4.4        Rcpp_1.0.9           
 [50] scattermore_0.8       vctrs_0.4.2           nlme_3.1-157          progressr_0.11.0      lmtest_0.9-40         spatstat.random_2.2-0 stringr_1.4.1        
 [57] xfun_0.33             globals_0.16.1        ps_1.7.1              mime_0.12             miniUI_0.1.1.1        lifecycle_1.0.1       irlba_2.3.5.1        
 [64] devtools_2.4.3        goftest_1.2-3         future_1.28.0         MASS_7.3-57           zoo_1.8-11            scales_1.2.1          spatstat.core_2.4-4  
 [71] spatstat.utils_3.0-1  promises_1.2.0.1      parallel_4.2.1        RColorBrewer_1.1-3    curl_4.3.3            gridExtra_2.3         memoise_2.0.1        
 [78] reticulate_1.26       pbapply_1.5-0         ggplot2_3.3.6         rpart_4.1.16          stringi_1.7.8         pkgbuild_1.3.1        shape_1.4.6          
 [85] rlang_1.0.4           pkgconfig_2.0.3       matrixStats_0.62.0    lattice_0.20-45       tensor_1.5            ROCR_1.0-11           purrr_0.3.5          
 [92] labeling_0.4.2        patchwork_1.1.1       htmlwidgets_1.5.4     cowplot_1.1.1         processx_3.7.0        tidyselect_1.2.0      parallelly_1.32.1    
 [99] RcppAnnoy_0.0.19      plyr_1.8.7            R6_2.5.1              generics_0.1.3        DBI_1.1.3             mgcv_1.8-40           pillar_1.8.1         
[106] withr_2.5.0           fitdistrplus_1.1-8    abind_1.4-5           survival_3.2-13       tibble_3.1.8          future.apply_1.9.1    crayon_1.5.2         
[113] KernSmooth_2.23-20    utf8_1.2.2            spatstat.geom_2.4-0   plotly_4.10.0         usethis_2.1.6         grid_4.2.1            data.table_1.14.2    
[120] callr_3.7.2           digest_0.6.30         xtable_1.8-4          tidyr_1.2.1           httpuv_1.6.6          munsell_0.5.0         viridisLite_0.4.1    
[127] sessioninfo_1.2.2 

Could you give me some help about it? Thanks. And my env info is above.

UboCA avatar Oct 28 '22 07:10 UboCA