Open SuperSe7enF opened 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
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。
谢谢王老师,已经跑通啦!
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
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~