Open csoneson opened 2 months ago
To reproduce:
library(scRNAseq) library(iSEE) library(iSEEu) library(scater) sce <- ReprocessedAllenData(assays = "tophat_counts", legacy = TRUE) sce <- logNormCounts(sce, exprs_values = "tophat_counts") sce <- runPCA(sce) iSEE(sce, initial = list(ReducedDimensionPlot(), DynamicMarkerTable()))
Session info
R version 4.4.0 (2024-04-24) Platform: aarch64-apple-darwin20 Running under: macOS Sonoma 14.6.1 Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.0 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/Zurich tzcode source: internal attached base packages: [1] stats4 stats graphics grDevices utils datasets methods base other attached packages: [1] shiny_1.9.1 scater_1.33.4 ggplot2_3.5.1 [4] scuttle_1.15.4 iSEEu_1.17.0 iSEEhex_1.7.0 [7] iSEE_2.17.3 scRNAseq_2.19.1 SingleCellExperiment_1.27.2 [10] SummarizedExperiment_1.35.1 Biobase_2.65.0 GenomicRanges_1.57.1 [13] GenomeInfoDb_1.41.1 IRanges_2.39.2 S4Vectors_0.43.2 [16] BiocGenerics_0.51.0 MatrixGenerics_1.17.0 matrixStats_1.3.0 loaded via a namespace (and not attached): [1] splines_4.4.0 later_1.3.2 BiocIO_1.15.2 bitops_1.0-8 [5] filelock_1.0.3 tibble_3.2.1 XML_3.99-0.17 lifecycle_1.0.4 [9] httr2_1.0.3 edgeR_4.3.10 doParallel_1.0.17 lattice_0.22-6 [13] ensembldb_2.29.1 crosstalk_1.2.1 alabaster.base_1.5.5 magrittr_2.0.3 [17] limma_3.61.9 sass_0.4.9 jquerylib_0.1.4 yaml_2.3.10 [21] metapod_1.13.0 httpuv_1.6.15 DBI_1.2.3 RColorBrewer_1.1-3 [25] abind_1.4-5 zlibbioc_1.51.1 purrr_1.0.2 AnnotationFilter_1.29.0 [29] RCurl_1.98-1.16 rappdirs_0.3.3 circlize_0.4.16 GenomeInfoDbData_1.2.12 [33] ggrepel_0.9.5 irlba_2.3.5.1 alabaster.sce_1.5.1 dqrng_0.4.1 [37] codetools_0.2-20 DelayedArray_0.31.11 DT_0.33 tidyselect_1.2.1 [41] shape_1.4.6.1 farver_2.1.2 UCSC.utils_1.1.0 ScaledMatrix_1.13.0 [45] viridis_0.6.5 shinyWidgets_0.8.6 BiocFileCache_2.13.0 GenomicAlignments_1.41.0 [49] jsonlite_1.8.8 GetoptLong_1.0.5 BiocNeighbors_1.23.0 iterators_1.0.14 [53] systemfonts_1.1.0 foreach_1.5.2 tools_4.4.0 ragg_1.3.2 [57] Rcpp_1.0.13 glue_1.7.0 gridExtra_2.3 SparseArray_1.5.31 [61] mgcv_1.9-1 dplyr_1.1.4 HDF5Array_1.33.6 gypsum_1.1.6 [65] shinydashboard_0.7.2 withr_3.0.1 BiocManager_1.30.23 fastmap_1.2.0 [69] bluster_1.15.0 rhdf5filters_1.17.0 fansi_1.0.6 shinyjs_2.1.0 [73] digest_0.6.37 rsvd_1.0.5 R6_2.5.1 mime_0.12 [77] textshaping_0.4.0 colorspace_2.1-1 listviewer_4.0.0 RSQLite_2.3.7 [81] utf8_1.2.4 generics_0.1.3 hexbin_1.28.3 rtracklayer_1.65.0 [85] httr_1.4.7 htmlwidgets_1.6.4 S4Arrays_1.5.7 pkgconfig_2.0.3 [89] gtable_0.3.5 blob_1.2.4 ComplexHeatmap_2.21.0 XVector_0.45.0 [93] htmltools_0.5.8.1 ProtGenerics_1.37.1 rintrojs_0.3.4 clue_0.3-65 [97] scales_1.3.0 alabaster.matrix_1.5.5 png_0.1-8 scran_1.33.1 [101] rjson_0.2.22 nlme_3.1-165 curl_5.2.1 shinyAce_0.4.2 [105] cachem_1.1.0 rhdf5_2.49.0 GlobalOptions_0.1.2 BiocVersion_3.20.0 [109] parallel_4.4.0 miniUI_0.1.1.1 vipor_0.4.7 AnnotationDbi_1.67.0 [113] restfulr_0.0.15 pillar_1.9.0 grid_4.4.0 alabaster.schemas_1.5.0 [117] vctrs_0.6.5 promises_1.3.0 BiocSingular_1.21.2 dbplyr_2.5.0 [121] beachmat_2.21.5 xtable_1.8-4 cluster_2.1.6 beeswarm_0.4.0 [125] GenomicFeatures_1.57.0 locfit_1.5-9.10 cli_3.6.3 compiler_4.4.0 [129] Rsamtools_2.21.1 rlang_1.1.4 crayon_1.5.3 labeling_0.4.3 [133] ggbeeswarm_0.7.2 alabaster.se_1.5.3 viridisLite_0.4.2 BiocParallel_1.39.0 [137] munsell_0.5.1 Biostrings_2.73.1 lazyeval_0.2.2 colourpicker_1.3.0 [141] Matrix_1.7-0 ExperimentHub_2.13.1 bit64_4.0.5 Rhdf5lib_1.27.0 [145] statmod_1.5.0 KEGGREST_1.45.1 alabaster.ranges_1.5.2 AnnotationHub_3.13.3 [149] fontawesome_0.5.2 igraph_2.0.3 memoise_2.0.1 bslib_0.8.0 [153] bit_4.0.5
The panel reacts only to its own UI inputs, but not to updates to the incoming selection.
To reproduce:
Session info