I attach the sample file for reproducibility:
samplefile.txt
lympho.combined.datt.t <- read.table(file = "samplefile.txt")
dataset <- wrap_expression(
counts = exp(lympho.combined.datt.t),
expression = lympho.combined.datt.t
)
guidelines <- guidelines_shiny(dataset)
The last command correctly renders the Shiny dashboard with the different methods yet it yields the following errors (warnings?):
template: :1:2: executing "" at <.OSType>: reflect: indirection through nil pointer to embedded struct field Info
Listening on http://0.0.0.0:4714
The `name` provided ('clock-o') does not correspond to a known icon
The `name` provided ('clock-o') does not correspond to a known icon
The `name` provided ('clock-o') does not correspond to a known icon
The `name` provided ('clock-o') does not correspond to a known icon
The `name` provided ('clock-o') does not correspond to a known icon
sessionInfo()
> sessionInfo()
R version 4.2.2 (2022-10-31)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Ventura 13.2.1
Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices datasets utils methods base
other attached packages:
[1] shiny_1.7.4 SeuratData_0.2.2 dyno_0.1.2 dynwrap_1.2.3
[5] dynplot_1.1.2 dynmethods_1.0.5 dynguidelines_1.0.1 dynfeature_1.0.1
[9] patchwork_1.1.2 SeuratObject_4.1.3 Seurat_4.3.0 dplyr_1.1.2
loaded via a namespace (and not attached):
[1] utf8_1.2.3 spatstat.explore_3.1-0 reticulate_1.28
[4] tidyselect_1.2.0 htmlwidgets_1.6.2 grid_4.2.2
[7] ranger_0.15.1 Rtsne_0.16 devtools_2.4.5
[10] munsell_0.5.0 codetools_0.2-19 ica_1.0-3
[13] future_1.32.0 miniUI_0.1.1.1 withr_2.5.0
[16] spatstat.random_3.1-4 colorspace_2.1-0 progressr_0.13.0
[19] rstudioapi_0.14 ROCR_1.0-11 tensor_1.5
[22] shinyWidgets_0.7.6 listenv_0.9.0 labeling_0.4.2
[25] polyclip_1.10-4 farver_2.1.1 rprojroot_2.0.3
[28] parallelly_1.35.0 vctrs_0.6.2 generics_0.1.3
[31] R6_2.5.1 GA_3.2.3 graphlayouts_1.0.0
[34] spatstat.utils_3.0-2 cachem_1.0.8 assertthat_0.2.1
[37] promises_1.2.0.1 scales_1.2.1 ggraph_2.1.0
[40] lmds_0.1.0 gtable_0.3.3 babelwhale_1.1.0
[43] globals_0.16.2 processx_3.8.1 goftest_1.2-3
[46] tidygraph_1.2.3 rlang_1.1.1 akima_0.6-3.4
[49] splines_4.2.2 lazyeval_0.2.2 spatstat.geom_3.1-0
[52] yaml_2.3.7 reshape2_1.4.4 abind_1.4-5
[55] httpuv_1.6.9 tools_4.2.2 usethis_2.1.6
[58] ggplot2_3.4.2 ellipsis_0.3.2 jquerylib_0.1.4
[61] RColorBrewer_1.1-3 sessioninfo_1.2.2 ggridges_0.5.4
[64] Rcpp_1.0.10 plyr_1.8.8 purrr_1.0.1
[67] ps_1.7.5 prettyunits_1.1.1 deldir_1.0-6
[70] pbapply_1.7-0 viridis_0.6.3 cowplot_1.1.1
[73] urlchecker_1.0.1 fontawesome_0.5.1 dynparam_1.0.2
[76] zoo_1.8-12 ggrepel_0.9.3 cluster_2.1.4
[79] fs_1.6.2 magrittr_2.0.3 data.table_1.14.8
[82] scattermore_0.8 carrier_0.1.1 lmtest_0.9-40
[85] RANN_2.6.1 fitdistrplus_1.1-11 matrixStats_0.63.0
[88] pkgload_1.3.2 hms_1.1.3 shinyjs_2.1.0
[91] mime_0.12 xtable_1.8-4 gridExtra_2.3
[94] testthat_3.1.8 compiler_4.2.2 tibble_3.2.1
[97] KernSmooth_2.23-20 crayon_1.5.2 htmltools_0.5.5
[100] proxyC_0.3.3 later_1.3.1 tzdb_0.3.0
[103] tidyr_1.3.0 RcppParallel_5.1.7 tweenr_2.0.2
[106] MASS_7.3-58.2 rappdirs_0.3.3 Matrix_1.5-3
[109] readr_2.1.4 brio_1.1.3 cli_3.6.1
[112] parallel_4.2.2 igraph_1.4.2 pkgconfig_2.0.3
[115] sp_1.6-0 plotly_4.10.1 spatstat.sparse_3.0-1
[118] foreach_1.5.2 bslib_0.4.2 dynutils_1.0.11
[121] stringr_1.5.0 callr_3.7.3 digest_0.6.31
[124] dyndimred_1.0.4 sctransform_0.3.5 RcppAnnoy_0.0.20
[127] spatstat.data_3.0-1 leiden_0.4.3 uwot_0.1.14
[130] curl_5.0.0 lifecycle_1.0.3 nlme_3.1-162
[133] jsonlite_1.8.4 desc_1.4.2 viridisLite_0.4.2
[136] fansi_1.0.4 pillar_1.9.0 lattice_0.20-45
[139] fastmap_1.1.1 httr_1.4.5 pkgbuild_1.4.0
[142] survival_3.5-3 waldo_0.5.0 glue_1.6.2
[145] remotes_2.4.2 png_0.1-8 iterators_1.0.14
[148] ggforce_0.4.1 stringi_1.7.12 sass_0.4.6
[151] profvis_0.3.8 memoise_2.0.1 renv_0.17.2
[154] irlba_2.3.5.1 future.apply_1.10.0
I attach the sample file for reproducibility:
samplefile.txt
The last command correctly renders the Shiny dashboard with the different methods yet it yields the following errors (warnings?):
sessionInfo()