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WangJin93 / TFTF

Transcription Factor Target Finder (TFTF) is an R package designed for predicting transcription factor target genes and predicting upstream transcription factors of target genes.
https://jingle.shinyapps.io/TF_Target_Finder/
MIT License
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predict_TF() 函数报错 #1

Open SuperSe7enF opened 2 months ago

SuperSe7enF commented 2 months ago

谢谢王老师开发的 TFTF 包！

王老师，我在运行 TFTF 中 predict_TF() 这个函数时遇到了下面的问题

Error in session$sendNotification("show", list(html = res$html, action = actionRes$html,  :
  不适用于非函数

简单检索了一下是 shiny 包中 showNotification() 函数导致的问题，但我不知道该如何修改

谢谢王老师的指导~


sessionInfo()
R version 4.3.1 (2023-06-16)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.6 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas/libblas.so.3 
LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.2.20.so;  LAPACK version 3.7.1

locale:
 [1] LC_CTYPE=zh_CN.UTF-8       LC_NUMERIC=C               LC_TIME=zh_CN.UTF-8       
 [4] LC_COLLATE=zh_CN.UTF-8     LC_MONETARY=zh_CN.UTF-8    LC_MESSAGES=zh_CN.UTF-8   
 [7] LC_PAPER=zh_CN.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
[10] LC_TELEPHONE=C             LC_MEASUREMENT=zh_CN.UTF-8 LC_IDENTIFICATION=C       

time zone: Asia/Shanghai
tzcode source: system (glibc)

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

other attached packages:
 [1] UCSCXenaTools_1.4.8         shiny_1.7.4                 ComplexHeatmap_2.16.0      
 [4] UCell_2.4.0                 GSEABase_1.62.0             graph_1.78.0               
 [7] annotate_1.78.0             XML_3.99-0.14               GSVA_1.48.1                
[10] progeny_1.22.0              treeio_1.24.1               ggtree_3.8.0               
[13] scuttle_1.10.1              corrplot_0.92               tradeSeq_1.14.0            
[16] plyr_1.8.8                  ggrepel_0.9.3               sscVis_0.1.0               
[19] slingshot_2.8.0             TrajectoryUtils_1.8.0       princurve_2.1.6            
[22] monocle3_1.3.1              SingleCellExperiment_1.22.0 SummarizedExperiment_1.30.2
[25] GenomicRanges_1.52.0        GenomeInfoDb_1.36.0         MatrixGenerics_1.12.2      
[28] matrixStats_1.0.0           COSG_0.9.0                  ggrastr_1.0.2              
[31] igraph_1.5.0                copykat_1.1.0               ggpubr_0.6.0               
[34] scRNAtoolVis_0.0.6          ClusterGVis_0.1.0           monocle_2.28.0             
[37] DDRTree_0.1.5               irlba_2.3.5.1               VGAM_1.1-8                 
[40] Matrix_1.6-0                ggpointdensity_0.1.0        viridis_0.6.3              
[43] viridisLite_0.4.2           scCustomize_1.1.1           RColorBrewer_1.1-3         
[46] DOSE_3.26.1                 ggsci_3.0.0                 reshape2_1.4.4             
[49] paletteer_1.5.0             org.Hs.eg.db_3.17.0         AnnotationDbi_1.62.1       
[52] IRanges_2.34.0              S4Vectors_0.38.1            Biobase_2.60.0             
[55] BiocGenerics_0.46.0         tidydr_0.0.5                Nebulosa_1.10.0            
[58] patchwork_1.1.3.9000        cowplot_1.1.1               clusterProfiler_4.8.3      
[61] lubridate_1.9.2             forcats_1.0.0               stringr_1.5.0              
[64] dplyr_1.1.2                 purrr_1.0.1                 tidyr_1.3.0                
[67] tibble_3.2.1                ggplot2_3.4.2               tidyverse_2.0.0            
[70] SeuratObject_4.1.3          Seurat_4.3.0                qs_0.25.5                  
[73] data.table_1.14.8           readr_2.1.4                 TFTF_0.1.0                 

loaded via a namespace (and not attached):
  [1] ica_1.0-3                 plotly_4.10.2             Formula_1.2-5            
  [4] rematch2_2.1.2            maps_3.4.1                devtools_2.4.5           
  [7] zlibbioc_1.46.0           tidyselect_1.2.0          bit_4.0.5                
 [10] doParallel_1.0.17         clue_0.3-64               lattice_0.21-8           
 [13] rjson_0.2.21              blob_1.2.4                urlchecker_1.0.1         
 [16] S4Arrays_1.2.1            parallel_4.3.1            png_0.1-8                
 [19] plotrix_3.8-2             cli_3.6.1                 ggplotify_0.1.2          
 [22] ppcor_1.1                 goftest_1.2-3             jjAnno_0.0.3             
 [25] org.Mm.eg.db_3.17.0       BiocNeighbors_1.18.0      dendextend_1.17.1        
 [28] uwot_0.1.14               shadowtext_0.1.2          curl_5.0.1               
 [31] mime_0.12                 evaluate_0.21             tidytree_0.4.2           
 [34] leiden_0.4.3              stringi_1.7.12            backports_1.4.1          
 [37] desc_1.4.2                httpuv_1.6.11             magrittr_2.0.3           
 [40] mclust_6.0.0              RApiSerialize_0.1.2       ggraph_2.1.0             
 [43] DT_0.28                   sctransform_0.3.5         ggbeeswarm_0.7.2         
 [46] sessioninfo_1.2.2         HDF5Array_1.28.1          DBI_1.1.3                
 [49] terra_1.7-39              moduleColor_1.8-4         withr_2.5.0              
 [52] rprojroot_2.0.3           enrichplot_1.20.0         lmtest_0.9-40            
 [55] tidygraph_1.2.3           formatR_1.14              BiocManager_1.30.21      
 [58] htmlwidgets_1.6.2         fs_1.6.2                  labeling_0.4.2           
 [61] sparsesvd_0.2-2           reticulate_1.34.0         zoo_1.8-12               
 [64] XVector_0.40.0            knitr_1.43                RhpcBLASctl_0.23-42      
 [67] docopt_0.7.1              timechange_0.2.0          foreach_1.5.2            
 [70] fansi_1.0.4               rhdf5_2.44.0              psych_2.3.9              
 [73] gridGraphics_0.5-1        ellipsis_0.3.2            lazyeval_0.2.2           
 [76] survival_3.5-5            scattermore_1.2           crayon_1.5.2             
 [79] RcppAnnoy_0.0.20          progressr_0.13.0          tweenr_2.0.2             
 [82] later_1.3.1               ggridges_0.5.6            codetools_0.2-19         
 [85] base64enc_0.1-3           GlobalOptions_0.1.2       profvis_0.3.8            
 [88] HSMMSingleCell_1.20.0     KEGGREST_1.40.0           Rtsne_0.16               
 [91] shape_1.4.6               fastICA_1.2-3             limma_3.56.2             
 [94] foreign_0.8-82            pkgconfig_2.0.3           aplot_0.1.10             
 [97] gridBase_0.4-7            spatstat.sparse_3.0-1     ape_5.7-1                
[100] xtable_1.8-4              car_3.1-2                 httr_1.4.6               
[103] tools_4.3.1               globals_0.16.2            pkgbuild_1.4.1           
[106] beeswarm_0.4.0            htmlTable_2.4.1           broom_1.0.5              
[109] checkmate_2.2.0           nlme_3.1-162              futile.logger_1.4.3      
[112] lambda.r_1.2.4            HDO.db_0.99.1             lme4_1.1-35.1            
[115] digest_0.6.31             farver_2.1.1              tzdb_0.4.0               
[118] ks_1.14.0                 yulab.utils_0.1.4         rpart_4.1.19             
[121] glue_1.6.2                cachem_1.0.8              VennDiagram_1.7.3        
[124] polyclip_1.10-4           UpSetR_1.4.0              Hmisc_5.1-0              
[127] generics_0.1.3            Biostrings_2.68.1         dynamicTreeCut_1.63-1    
[130] mvtnorm_1.2-2             parallelly_1.36.0         pkgload_1.3.2            
[133] mnormt_2.1.1              impute_1.74.1             ScaledMatrix_1.8.1       
[136] carData_3.0-5             minqa_1.2.5               pbapply_1.7-0            
[139] fields_15.2               spam_2.10-0               gson_0.1.0               
[142] utf8_1.2.3                graphlayouts_1.0.0        ggsignif_0.6.4           
[145] gridExtra_2.3             GenomeInfoDbData_1.2.10   rhdf5filters_1.12.1      
[148] RCurl_1.98-1.12           memoise_2.0.1             rmarkdown_2.22           
[151] pheatmap_1.0.12           downloader_0.4            scales_1.3.0             
[154] future_1.32.0             RANN_2.6.1                stringfish_0.15.8        
[157] spatstat.data_3.0-1       rstudioapi_0.14           cluster_2.1.4            
[160] janitor_2.2.0             spatstat.utils_3.0-3      hms_1.1.3                
[163] fitdistrplus_1.1-11       munsell_0.5.0             colorspace_2.1-0         
[166] rlang_1.1.1               ggdendro_0.1.23           sparseMatrixStats_1.12.0 
[169] DelayedMatrixStats_1.22.1 dotCall64_1.1-1           ggforce_0.4.1            
[172] circlize_0.4.15           mgcv_1.9-0                xfun_0.39                
[175] remotes_2.4.2             iterators_1.0.14          abind_1.4-5              
[178] GOSemSim_2.26.1           Rhdf5lib_1.22.0           futile.options_1.0.1     
[181] bitops_1.0-7              ps_1.7.5                  promises_1.2.0.1         
[184] scatterpie_0.2.1          RSQLite_2.3.1             leidenbase_0.1.25        
[187] qvalue_2.32.0             qlcMatrix_0.9.7           fgsea_1.26.0             
[190] DelayedArray_0.26.3       GO.db_3.17.0              compiler_4.3.1           
[193] prettyunits_1.1.1         beachmat_2.16.0           boot_1.3-28              
[196] listenv_0.9.0             Rcpp_1.0.10               BiocSingular_1.16.0      
[199] edgeR_3.42.4              tensor_1.5                usethis_2.2.1            
[202] MASS_7.3-60               BiocParallel_1.34.2       spatstat.random_3.1-5    
[205] R6_2.5.1                  fastmap_1.1.1             fastmatch_1.1-3          
[208] rstatix_0.7.2             vipor_0.4.5               ROCR_1.0-11              
[211] rsvd_1.0.5                nnet_7.3-19               gtable_0.3.3             
[214] KernSmooth_2.23-22        miniUI_0.1.1.1            deldir_1.0-9             
[217] htmltools_0.5.5           RcppParallel_5.1.7        bit64_4.0.5              
[220] spatstat.explore_3.2-1    lifecycle_1.0.3           ggprism_1.0.4            
[223] processx_3.8.1            nloptr_2.0.3              callr_3.7.3              
[226] vctrs_0.6.3               slam_0.1-50               spatstat.geom_3.2-1      
[229] snakecase_0.11.0          ggfun_0.1.0               sp_1.6-1                 
[232] UCSCXenaShiny_2.1.0       future.apply_1.11.0       pracma_2.4.2             
[235] pillar_1.9.0              locfit_1.5-9.8            combinat_0.0-8           
[238] jsonlite_1.8.5            GetoptLong_1.0.5
WangJin93 commented 2 months ago

感谢您的反馈，已更新函数。原因在于原先这个函数是用于shiny app的，showNotification函数只能在App中运行，改成R语言函数的时候有部分数据集的检索代码忘记改了。

SuperSe7enF commented 2 months ago

谢谢王老师，已经跑通啦！