search

SGDDNB / ShinyCell

Shiny Interactive Web Apps for Single-Cell Data
GNU General Public License v3.0
148 stars 57 forks source link

quotations instead of labels #82

Open kenneditodd opened 8 months ago

kenneditodd commented 8 months ago

Hello,

I installed ShinyCell using devtools::install_github("SGDDNB/ShinyCell", ref = remotes::github_pull(80))

I have the following packages loaded.

other attached packages:
 [1] ggdendro_0.1.23    ggrepel_0.9.4      magrittr_2.0.3     DT_0.31            shinyhelper_0.3.2 
 [6] shiny_1.8.0        tidyr_1.3.0        ShinyCell_2.1.0    RColorBrewer_1.1-3 readr_2.1.4       
[11] glue_1.6.2         R.utils_2.12.3     R.oo_1.25.0        R.methodsS3_1.8.2  reticulate_1.34.0 
[16] hdf5r_1.3.8        Matrix_1.6-4       data.table_1.14.10 plotly_4.10.3      ggplot2_3.4.4     
[21] gtools_3.9.5       gridExtra_2.3      ggtree_3.9.0.001   dplyr_1.1.3        Seurat_5.0.1      
[26] SeuratObject_5.0.1 sp_2.1-2

I am using seurat v5 with the option options(Seurat.object.assay.version = "v4").

I am able to create a shiny app by running createConf() followed by makeShinyApp(). When I run my app, it can visualize the UMAP heatmap. However, there is an error with the x-axis, y-axis, and legend labels. For example, instead of 'umap1', I just see what looks like a bunch of quotations (" " " ").

Any thoughts on what could cause this?

kenneditodd commented 8 months ago

The app runs correctly on my local RStudio but not my cloud based RStudio. Here's the devtools::session_info() for my environment that worked and that didn't work.

My environment that worked

─ Session info ──────────────────────────────────────────────────────────────────────────────────────────────
 setting  value
 version  R version 4.2.1 (2022-06-23)
 os       macOS Ventura 13.6.1
 system   x86_64, darwin17.0
 ui       RStudio
 language (EN)
 collate  en_US.UTF-8
 ctype    en_US.UTF-8
 tz       America/Phoenix
 date     2024-01-02
 rstudio  2023.06.2+561 Mountain Hydrangea (desktop)
 pandoc   NA

─ Packages ──────────────────────────────────────────────────────────────────────────────────────────────────
 package     * version date (UTC) lib source
 bit           4.0.5   2022-11-15 [1] CRAN (R 4.2.0)
 bit64         4.0.5   2020-08-30 [1] CRAN (R 4.2.0)
 bslib         0.5.1   2023-08-11 [1] CRAN (R 4.2.0)
 cachem        1.0.8   2023-05-01 [1] CRAN (R 4.2.0)
 callr         3.7.3   2022-11-02 [1] CRAN (R 4.2.0)
 cli           3.6.1   2023-03-23 [1] CRAN (R 4.2.0)
 colorspace    2.1-0   2023-01-23 [1] CRAN (R 4.2.0)
 crayon        1.5.2   2022-09-29 [1] CRAN (R 4.2.0)
 crosstalk     1.2.0   2021-11-04 [1] CRAN (R 4.2.0)
 data.table  * 1.14.8  2023-02-17 [1] CRAN (R 4.2.0)
 devtools      2.4.5   2022-10-11 [1] CRAN (R 4.2.0)
 digest        0.6.33  2023-07-07 [1] CRAN (R 4.2.0)
 dplyr         1.1.3   2023-09-03 [1] CRAN (R 4.2.0)
 DT          * 0.29    2023-08-29 [1] CRAN (R 4.2.0)
 ellipsis      0.3.2   2021-04-29 [1] CRAN (R 4.2.0)
 fansi         1.0.4   2023-01-22 [1] CRAN (R 4.2.0)
 farver        2.1.1   2022-07-06 [1] CRAN (R 4.2.0)
 fastmap       1.1.1   2023-02-24 [1] CRAN (R 4.2.0)
 fontawesome   0.5.2   2023-08-19 [1] CRAN (R 4.2.0)
 fs            1.6.3   2023-07-20 [1] CRAN (R 4.2.0)
 generics      0.1.3   2022-07-05 [1] CRAN (R 4.2.0)
 ggdendro    * 0.1.23  2022-02-16 [1] CRAN (R 4.2.0)
 ggplot2     * 3.4.3   2023-08-14 [1] CRAN (R 4.2.0)
 ggrepel     * 0.9.3   2023-02-03 [1] CRAN (R 4.2.0)
 glue          1.6.2   2022-02-24 [1] CRAN (R 4.2.0)
 gridExtra   * 2.3     2017-09-09 [1] CRAN (R 4.2.0)
 gtable        0.3.4   2023-08-21 [1] CRAN (R 4.2.0)
 hdf5r       * 1.3.8   2023-01-21 [1] CRAN (R 4.2.0)
 htmltools     0.5.6   2023-08-10 [1] CRAN (R 4.2.0)
 htmlwidgets   1.6.2   2023-03-17 [1] CRAN (R 4.2.0)
 httpuv        1.6.11  2023-05-11 [1] CRAN (R 4.2.0)
 jquerylib     0.1.4   2021-04-26 [1] CRAN (R 4.2.0)
 jsonlite      1.8.7   2023-06-29 [1] CRAN (R 4.2.0)
 labeling      0.4.3   2023-08-29 [1] CRAN (R 4.2.0)
 later         1.3.1   2023-05-02 [1] CRAN (R 4.2.0)
 lattice       0.21-8  2023-04-05 [1] CRAN (R 4.2.0)
 lifecycle     1.0.3   2022-10-07 [1] CRAN (R 4.2.0)
 magrittr    * 2.0.3   2022-03-30 [1] CRAN (R 4.2.0)
 MASS          7.3-60  2023-05-04 [1] CRAN (R 4.2.0)
 Matrix      * 1.4-1   2022-03-23 [1] CRAN (R 4.2.1)
 memoise       2.0.1   2021-11-26 [1] CRAN (R 4.2.0)
 mime          0.12    2021-09-28 [1] CRAN (R 4.2.0)
 miniUI        0.1.1.1 2018-05-18 [1] CRAN (R 4.2.0)
 munsell       0.5.0   2018-06-12 [1] CRAN (R 4.2.0)
 pillar        1.9.0   2023-03-22 [1] CRAN (R 4.2.0)
 pkgbuild      1.4.2   2023-06-26 [1] CRAN (R 4.2.0)
 pkgconfig     2.0.3   2019-09-22 [1] CRAN (R 4.2.0)
 pkgload       1.3.2.1 2023-07-08 [1] CRAN (R 4.2.0)
 prettyunits   1.1.1   2020-01-24 [1] CRAN (R 4.2.0)
 processx      3.8.2   2023-06-30 [1] CRAN (R 4.2.0)
 profvis       0.3.8   2023-05-02 [1] CRAN (R 4.2.0)
 promises      1.2.1   2023-08-10 [1] CRAN (R 4.2.0)
 ps            1.7.5   2023-04-18 [1] CRAN (R 4.2.0)
 purrr         1.0.2   2023-08-10 [1] CRAN (R 4.2.0)
 R6            2.5.1   2021-08-19 [1] CRAN (R 4.2.0)
 ragg          1.2.5   2023-01-12 [1] CRAN (R 4.2.0)
 Rcpp          1.0.11  2023-07-06 [1] CRAN (R 4.2.0)
 remotes       2.4.2.1 2023-07-18 [1] CRAN (R 4.2.0)
 rlang         1.1.1   2023-04-28 [1] CRAN (R 4.2.0)
 rsconnect     1.1.0   2023-09-05 [1] CRAN (R 4.2.0)
 rstudioapi    0.15.0  2023-07-07 [1] CRAN (R 4.2.0)
 sass          0.4.7   2023-07-15 [1] CRAN (R 4.2.0)
 scales        1.2.1   2022-08-20 [1] CRAN (R 4.2.0)
 sessioninfo   1.2.2   2021-12-06 [1] CRAN (R 4.2.0)
 shiny       * 1.7.5   2023-08-12 [1] CRAN (R 4.2.0)
 shinyhelper * 0.3.2   2019-11-09 [1] CRAN (R 4.2.0)
 stringi       1.7.12  2023-01-11 [1] CRAN (R 4.2.0)
 stringr       1.5.0   2022-12-02 [1] CRAN (R 4.2.0)
 systemfonts   1.0.4   2022-02-11 [1] CRAN (R 4.2.0)
 textshaping   0.3.6   2021-10-13 [1] CRAN (R 4.2.0)
 tibble        3.2.1   2023-03-20 [1] CRAN (R 4.2.0)
 tidyselect    1.2.0   2022-10-10 [1] CRAN (R 4.2.0)
 urlchecker    1.0.1   2021-11-30 [1] CRAN (R 4.2.0)
 usethis       2.2.2   2023-07-06 [1] CRAN (R 4.2.0)
 utf8          1.2.3   2023-01-31 [1] CRAN (R 4.2.0)
 vctrs         0.6.3   2023-06-14 [1] CRAN (R 4.2.0)
 withr         2.5.0   2022-03-03 [1] CRAN (R 4.2.0)
 xtable        1.8-4   2019-04-21 [1] CRAN (R 4.2.0)
 yaml          2.3.7   2023-01-23 [1] CRAN (R 4.2.0)

My environment that did not work.

─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────
 setting  value
 version  R version 4.2.2 (2022-10-31)
 os       Red Hat Enterprise Linux 8.8 (Ootpa)
 system   x86_64, linux-gnu
 ui       RStudio
 language (EN)
 collate  en_US.UTF-8
 ctype    en_US.UTF-8
 tz       America/Chicago
 date     2024-01-02
 rstudio  2022.12.0+353.pro20 Elsbeth Geranium (server)
 pandoc   NA

─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
 package     * version date (UTC) lib source
 bit           4.0.5   2022-11-15 [2] CRAN (R 4.2.2)
 bit64         4.0.5   2020-08-30 [2] CRAN (R 4.2.2)
 bslib         0.6.1   2023-11-28 [2] CRAN (R 4.2.2)
 cachem        1.0.8   2023-05-01 [2] CRAN (R 4.2.2)
 cli           3.6.2   2023-12-11 [2] CRAN (R 4.2.2)
 colorspace    2.1-0   2023-01-23 [2] CRAN (R 4.2.2)
 crayon        1.5.2   2022-09-29 [2] CRAN (R 4.2.2)
 crosstalk     1.2.1   2023-11-23 [2] CRAN (R 4.2.2)
 data.table  * 1.14.10 2023-12-08 [1] CRAN (R 4.2.2)
 devtools      2.4.5   2022-10-11 [2] CRAN (R 4.2.2)
 digest        0.6.33  2023-07-07 [2] CRAN (R 4.2.2)
 dplyr         1.1.3   2023-09-03 [1] CRAN (R 4.2.2)
 DT          * 0.31    2023-12-09 [2] CRAN (R 4.2.2)
 ellipsis      0.3.2   2021-04-29 [2] CRAN (R 4.2.2)
 fansi         1.0.6   2023-12-08 [2] CRAN (R 4.2.2)
 farver        2.1.1   2022-07-06 [2] CRAN (R 4.2.2)
 fastmap       1.1.1   2023-02-24 [2] CRAN (R 4.2.2)
 fontawesome   0.5.2   2023-08-19 [2] CRAN (R 4.2.2)
 fs            1.6.3   2023-07-20 [2] CRAN (R 4.2.2)
 generics      0.1.3   2022-07-05 [2] CRAN (R 4.2.2)
 ggdendro    * 0.1.23  2022-02-16 [2] CRAN (R 4.2.2)
 ggplot2     * 3.4.4   2023-10-12 [1] CRAN (R 4.2.2)
 ggrepel     * 0.9.4   2023-10-13 [2] CRAN (R 4.2.2)
 glue          1.6.2   2022-02-24 [2] CRAN (R 4.2.2)
 gridExtra   * 2.3     2017-09-09 [2] CRAN (R 4.2.2)
 gtable        0.3.4   2023-08-21 [2] CRAN (R 4.2.2)
 hdf5r       * 1.3.8   2023-01-21 [2] CRAN (R 4.2.2)
 htmltools     0.5.7   2023-11-03 [1] CRAN (R 4.2.2)
 htmlwidgets   1.6.4   2023-12-06 [2] CRAN (R 4.2.2)
 httpuv        1.6.13  2023-12-06 [2] CRAN (R 4.2.2)
 jquerylib     0.1.4   2021-04-26 [2] CRAN (R 4.2.2)
 jsonlite      1.8.8   2023-12-04 [2] CRAN (R 4.2.2)
 labeling      0.4.3   2023-08-29 [2] CRAN (R 4.2.2)
 later         1.3.2   2023-12-06 [2] CRAN (R 4.2.2)
 lattice       0.20-45 2021-09-22 [3] CRAN (R 4.2.2)
 lifecycle     1.0.4   2023-11-07 [2] CRAN (R 4.2.2)
 magrittr    * 2.0.3   2022-03-30 [2] CRAN (R 4.2.2)
 MASS          7.3-60  2023-05-04 [2] CRAN (R 4.2.2)
 Matrix      * 1.6-4   2023-11-30 [2] CRAN (R 4.2.2)
 memoise       2.0.1   2021-11-26 [2] CRAN (R 4.2.2)
 mime          0.12    2021-09-28 [2] CRAN (R 4.2.2)
 miniUI        0.1.1.1 2018-05-18 [2] CRAN (R 4.2.2)
 munsell       0.5.0   2018-06-12 [2] CRAN (R 4.2.2)
 pillar        1.9.0   2023-03-22 [2] CRAN (R 4.2.2)
 pkgbuild      1.4.3   2023-12-10 [2] CRAN (R 4.2.2)
 pkgconfig     2.0.3   2019-09-22 [2] CRAN (R 4.2.2)
 pkgload       1.3.3   2023-09-22 [2] CRAN (R 4.2.2)
 profvis       0.3.8   2023-05-02 [2] CRAN (R 4.2.2)
 promises      1.2.1   2023-08-10 [2] CRAN (R 4.2.2)
 purrr         1.0.2   2023-08-10 [2] CRAN (R 4.2.2)
 R6            2.5.1   2021-08-19 [2] CRAN (R 4.2.2)
 ragg          1.2.7   2023-12-11 [2] CRAN (R 4.2.2)
 Rcpp          1.0.11  2023-07-06 [2] CRAN (R 4.2.2)
 remotes       2.4.2.1 2023-07-18 [2] CRAN (R 4.2.2)
 rlang         1.1.2   2023-11-04 [2] CRAN (R 4.2.2)
 rsconnect     1.1.1   2023-10-04 [2] CRAN (R 4.2.2)
 rstudioapi    0.15.0  2023-07-07 [2] CRAN (R 4.2.2)
 sass          0.4.8   2023-12-06 [2] CRAN (R 4.2.2)
 scales        1.3.0   2023-11-28 [1] CRAN (R 4.2.2)
 sessioninfo   1.2.2   2021-12-06 [2] CRAN (R 4.2.2)
 shiny       * 1.8.0   2023-11-17 [2] CRAN (R 4.2.2)
 shinyhelper * 0.3.2   2019-11-09 [2] CRAN (R 4.2.2)
 stringi       1.8.3   2023-12-11 [2] CRAN (R 4.2.2)
 stringr       1.5.1   2023-11-14 [2] CRAN (R 4.2.2)
 systemfonts   1.0.5   2023-10-09 [2] CRAN (R 4.2.2)
 textshaping   0.3.7   2023-10-09 [2] CRAN (R 4.2.2)
 tibble        3.2.1   2023-03-20 [2] CRAN (R 4.2.2)
 tidyselect    1.2.0   2022-10-10 [2] CRAN (R 4.2.2)
 urlchecker    1.0.1   2021-11-30 [2] CRAN (R 4.2.2)
 usethis       2.2.2   2023-07-06 [2] CRAN (R 4.2.2)
 utf8          1.2.4   2023-10-22 [2] CRAN (R 4.2.2)
 vctrs         0.6.5   2023-12-01 [2] CRAN (R 4.2.2)
 withr         2.5.2   2023-10-30 [2] CRAN (R 4.2.2)
 xtable        1.8-4   2019-04-21 [2] CRAN (R 4.2.2)
 yaml          2.3.7   2023-01-23 [1] CRAN (R 4.2.2)