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LieberInstitute / spatialLIBD

Code for the spatialLIBD R/Bioconductor package and shiny app
http://LieberInstitute.github.io/spatialLIBD/
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Cannot plot annotations/discrete variables #14

Closed dimitriDA closed 2 years ago

dimitriDA commented 3 years ago

Hi, when running the shiny app I try to set my own annotations as default but the original data's annotations (clusters 1-12 and layers 1-6) still show in the cluster static. I tried loading them again as a separate discrete value and select that in my app but the original annotations are also plotted instead.

full R session information.

─ Session info ───────────────────────────────────────────────────────────────
 setting  value                       
 version  R version 4.1.0 (2021-05-18)
 os       Ubuntu 20.04.2 LTS          
 system   x86_64, linux-gnu           
 ui       X11                         
 language (EN)                        
 collate  en_US.UTF-8                 
 ctype    en_US.UTF-8                 
 tz       Etc/UTC                     
 date     2021-07-07                  

─ Packages ───────────────────────────────────────────────────────────────────
 package                * version  date       lib source        
 AnnotationDbi            1.54.1   2021-06-08 [1] Bioconductor  
 AnnotationHub            3.0.1    2021-06-20 [1] Bioconductor  
 assertthat               0.2.1    2019-03-21 [1] CRAN (R 4.1.0)
 attempt                  0.3.1    2020-05-03 [1] CRAN (R 4.1.0)
 beachmat                 2.8.0    2021-05-19 [1] Bioconductor  
 beeswarm                 0.4.0    2021-06-01 [1] CRAN (R 4.1.0)
 benchmarkme              1.0.7    2021-03-21 [1] CRAN (R 4.1.0)
 benchmarkmeData          1.0.4    2020-04-23 [1] CRAN (R 4.1.0)
 Biobase                * 2.52.0   2021-05-19 [1] Bioconductor  
 BiocFileCache          * 2.0.0    2021-05-19 [1] Bioconductor  
 BiocGenerics           * 0.38.0   2021-05-19 [1] Bioconductor  
 BiocIO                   1.2.0    2021-05-19 [1] Bioconductor  
 BiocManager            * 1.30.16  2021-06-15 [1] CRAN (R 4.1.0)
 BiocNeighbors            1.10.0   2021-05-19 [1] Bioconductor  
 BiocParallel             1.26.0   2021-05-19 [1] Bioconductor  
 BiocSingular             1.8.1    2021-06-08 [1] Bioconductor  
 BiocVersion              3.13.1   2021-03-19 [1] Bioconductor  
 Biostrings               2.60.1   2021-06-06 [1] Bioconductor  
 bit                      4.0.4    2020-08-04 [1] CRAN (R 4.1.0)
 bit64                    4.0.5    2020-08-30 [1] CRAN (R 4.1.0)
 bitops                   1.0-7    2021-04-24 [1] CRAN (R 4.1.0)
 blob                     1.2.1    2020-01-20 [1] CRAN (R 4.1.0)
 bslib                    0.2.5.1  2021-05-18 [1] CRAN (R 4.1.0)
 cachem                   1.0.5    2021-05-15 [1] CRAN (R 4.1.0)
 cli                      2.5.0    2021-04-26 [1] CRAN (R 4.1.0)
 codetools                0.2-18   2020-11-04 [1] CRAN (R 4.1.0)
 colorspace               2.0-1    2021-05-04 [1] CRAN (R 4.1.0)
 config                   0.3.1    2020-12-17 [1] CRAN (R 4.1.0)
 cowplot                  1.1.1    2020-12-30 [1] CRAN (R 4.1.0)
 crayon                   1.4.1    2021-02-08 [1] CRAN (R 4.1.0)
 curl                     4.3.1    2021-04-30 [1] CRAN (R 4.1.0)
 data.table               1.14.0   2021-02-21 [1] CRAN (R 4.1.0)
 DBI                      1.1.1    2021-01-15 [1] CRAN (R 4.1.0)
 dbplyr                 * 2.1.1    2021-04-06 [1] CRAN (R 4.1.0)
 DelayedArray             0.18.0   2021-05-19 [1] Bioconductor  
 DelayedMatrixStats       1.14.0   2021-05-19 [1] Bioconductor  
 desc                     1.3.0    2021-03-05 [1] CRAN (R 4.1.0)
 digest                   0.6.27   2020-10-24 [1] CRAN (R 4.1.0)
 dockerfiler              0.1.3    2019-03-19 [1] CRAN (R 4.1.0)
 doParallel               1.0.16   2020-10-16 [1] CRAN (R 4.1.0)
 dotCall64                1.0-1    2021-02-11 [1] CRAN (R 4.1.0)
 dplyr                    1.0.7    2021-06-18 [1] CRAN (R 4.1.0)
 dqrng                    0.3.0    2021-05-01 [1] CRAN (R 4.1.0)
 DropletUtils             1.12.1   2021-06-01 [1] Bioconductor  
 DT                       0.18     2021-04-14 [1] CRAN (R 4.1.0)
 edgeR                    3.34.0   2021-05-19 [1] Bioconductor  
 ellipsis                 0.3.2    2021-04-29 [1] CRAN (R 4.1.0)
 ExperimentHub            2.0.0    2021-05-19 [1] Bioconductor  
 fansi                    0.5.0    2021-05-25 [1] CRAN (R 4.1.0)
 fastmap                  1.1.0    2021-01-25 [1] CRAN (R 4.1.0)
 fields                   12.3     2021-05-17 [1] CRAN (R 4.1.0)
 filelock                 1.0.2    2018-10-05 [1] CRAN (R 4.1.0)
 foreach                  1.5.1    2020-10-15 [1] CRAN (R 4.1.0)
 fs                       1.5.0    2020-07-31 [1] CRAN (R 4.1.0)
 generics                 0.1.0    2020-10-31 [1] CRAN (R 4.1.0)
 GenomeInfoDb           * 1.28.0   2021-05-19 [1] Bioconductor  
 GenomeInfoDbData         1.2.6    2021-05-19 [1] Bioconductor  
 GenomicAlignments        1.28.0   2021-05-19 [1] Bioconductor  
 GenomicRanges          * 1.44.0   2021-05-19 [1] Bioconductor  
 ggbeeswarm               0.6.0    2017-08-07 [1] CRAN (R 4.1.0)
 ggplot2                  3.3.4    2021-06-16 [1] CRAN (R 4.1.0)
 glue                     1.4.2    2020-08-27 [1] CRAN (R 4.1.0)
 golem                    0.3.1    2021-04-17 [1] CRAN (R 4.1.0)
 gridExtra                2.3      2017-09-09 [1] CRAN (R 4.1.0)
 gtable                   0.3.0    2019-03-25 [1] CRAN (R 4.1.0)
 HDF5Array                1.20.0   2021-05-19 [1] Bioconductor  
 htmltools                0.5.1.1  2021-01-22 [1] CRAN (R 4.1.0)
 htmlwidgets              1.5.3    2020-12-10 [1] CRAN (R 4.1.0)
 httpuv                   1.6.1    2021-05-07 [1] CRAN (R 4.1.0)
 httr                     1.4.2    2020-07-20 [1] CRAN (R 4.1.0)
 interactiveDisplayBase   1.30.0   2021-05-19 [1] Bioconductor  
 IRanges                * 2.26.0   2021-05-19 [1] Bioconductor  
 irlba                    2.3.3    2019-02-05 [1] CRAN (R 4.1.0)
 iterators                1.0.13   2020-10-15 [1] CRAN (R 4.1.0)
 jquerylib                0.1.4    2021-04-26 [1] CRAN (R 4.1.0)
 jsonlite                 1.7.2    2020-12-09 [1] CRAN (R 4.1.0)
 KEGGREST                 1.32.0   2021-05-19 [1] Bioconductor  
 knitr                    1.33     2021-04-24 [1] CRAN (R 4.1.0)
 later                    1.2.0    2021-04-23 [1] CRAN (R 4.1.0)
 lattice                  0.20-44  2021-05-02 [1] CRAN (R 4.1.0)
 lazyeval                 0.2.2    2019-03-15 [1] CRAN (R 4.1.0)
 lifecycle                1.0.0    2021-02-15 [1] CRAN (R 4.1.0)
 limma                    3.48.0   2021-05-19 [1] Bioconductor  
 locfit                   1.5-9.4  2020-03-25 [1] CRAN (R 4.1.0)
 magick                   2.7.2    2021-05-02 [1] CRAN (R 4.1.0)
 magrittr                 2.0.1    2020-11-17 [1] CRAN (R 4.1.0)
 maps                     3.3.0    2018-04-03 [1] CRAN (R 4.1.0)
 markdown                 1.1      2019-08-07 [1] CRAN (R 4.1.0)
 Matrix                 * 1.3-3    2021-05-04 [1] CRAN (R 4.1.0)
 MatrixGenerics         * 1.4.0    2021-05-19 [1] Bioconductor  
 matrixStats            * 0.59.0   2021-06-01 [1] CRAN (R 4.1.0)
 memoise                  2.0.0    2021-01-26 [1] CRAN (R 4.1.0)
 mime                     0.10     2021-02-13 [1] CRAN (R 4.1.0)
 munsell                  0.5.0    2018-06-12 [1] CRAN (R 4.1.0)
 pillar                   1.6.1    2021-05-16 [1] CRAN (R 4.1.0)
 pkgconfig                2.0.3    2019-09-22 [1] CRAN (R 4.1.0)
 pkgload                  1.2.1    2021-04-06 [1] CRAN (R 4.1.0)
 plotly                   4.9.4.1  2021-06-18 [1] CRAN (R 4.1.0)
 png                      0.1-7    2013-12-03 [1] CRAN (R 4.1.0)
 Polychrome               1.2.6    2020-11-11 [1] CRAN (R 4.1.0)
 promises                 1.2.0.1  2021-02-11 [1] CRAN (R 4.1.0)
 pryr                   * 0.1.4    2018-02-18 [1] CRAN (R 4.1.0)
 purrr                    0.3.4    2020-04-17 [1] CRAN (R 4.1.0)
 R.methodsS3              1.8.1    2020-08-26 [1] CRAN (R 4.1.0)
 R.oo                     1.24.0   2020-08-26 [1] CRAN (R 4.1.0)
 R.utils                  2.10.1   2020-08-26 [1] CRAN (R 4.1.0)
 R6                       2.5.0    2020-10-28 [1] CRAN (R 4.1.0)
 rappdirs                 0.3.3    2021-01-31 [1] CRAN (R 4.1.0)
 RColorBrewer             1.1-2    2014-12-07 [1] CRAN (R 4.1.0)
 Rcpp                     1.0.6    2021-01-15 [1] CRAN (R 4.1.0)
 RCurl                    1.98-1.3 2021-03-16 [1] CRAN (R 4.1.0)
 remotes                  2.4.0    2021-06-02 [1] CRAN (R 4.1.0)
 restfulr                 0.0.13   2017-08-06 [1] CRAN (R 4.1.0)
 rhdf5                    2.36.0   2021-05-19 [1] Bioconductor  
 rhdf5filters             1.4.0    2021-05-19 [1] Bioconductor  
 Rhdf5lib                 1.14.1   2021-06-08 [1] Bioconductor  
 rjson                    0.2.20   2018-06-08 [1] CRAN (R 4.1.0)
 rlang                    0.4.11   2021-04-30 [1] CRAN (R 4.1.0)
 roxygen2                 7.1.1    2020-06-27 [1] CRAN (R 4.1.0)
 rprojroot                2.0.2    2020-11-15 [1] CRAN (R 4.1.0)
 Rsamtools                2.8.0    2021-05-19 [1] Bioconductor  
 rsconnect              * 0.8.18   2021-05-24 [1] CRAN (R 4.1.0)
 RSQLite                  2.2.7    2021-04-22 [1] CRAN (R 4.1.0)
 rstudioapi               0.13     2020-11-12 [1] CRAN (R 4.1.0)
 rsvd                     1.0.5    2021-04-16 [1] CRAN (R 4.1.0)
 rtracklayer            * 1.52.0   2021-05-19 [1] Bioconductor  
 S4Vectors              * 0.30.0   2021-05-19 [1] Bioconductor  
 sass                     0.4.0    2021-05-12 [1] CRAN (R 4.1.0)
 ScaledMatrix             1.0.0    2021-05-19 [1] Bioconductor  
 scales                   1.1.1    2020-05-11 [1] CRAN (R 4.1.0)
 scater                   1.20.1   2021-06-15 [1] Bioconductor  
 scatterplot3d            0.3-41   2018-03-14 [1] CRAN (R 4.1.0)
 scuttle                  1.2.0    2021-05-19 [1] Bioconductor  
 sessioninfo              1.1.1    2018-11-05 [1] CRAN (R 4.1.0)
 shiny                  * 1.6.0    2021-01-25 [1] CRAN (R 4.1.0)
 shinyWidgets             0.6.0    2021-03-15 [1] CRAN (R 4.1.0)
 SingleCellExperiment   * 1.14.1   2021-05-21 [1] Bioconductor  
 spam                     2.6-0    2020-12-14 [1] CRAN (R 4.1.0)
 sparseMatrixStats        1.4.0    2021-05-19 [1] Bioconductor  
 SpatialExperiment      * 1.2.1    2021-06-10 [1] Bioconductor  
 spatialLIBD            * 1.4.0    2021-05-20 [1] Bioconductor  
 stringi                  1.6.1    2021-05-10 [1] CRAN (R 4.1.0)
 stringr                  1.4.0    2019-02-10 [1] CRAN (R 4.1.0)
 SummarizedExperiment   * 1.22.0   2021-05-19 [1] Bioconductor  
 testthat                 3.0.3    2021-06-16 [1] CRAN (R 4.1.0)
 tibble                   3.1.2    2021-05-16 [1] CRAN (R 4.1.0)
 tidyr                    1.1.3    2021-03-03 [1] CRAN (R 4.1.0)
 tidyselect               1.1.1    2021-04-30 [1] CRAN (R 4.1.0)
 usethis                  2.0.1    2021-02-10 [1] CRAN (R 4.1.0)
 utf8                     1.2.1    2021-03-12 [1] CRAN (R 4.1.0)
 vctrs                    0.3.8    2021-04-29 [1] CRAN (R 4.1.0)
 vipor                    0.4.5    2017-03-22 [1] CRAN (R 4.1.0)
 viridis                  0.6.1    2021-05-11 [1] CRAN (R 4.1.0)
 viridisLite              0.4.0    2021-04-13 [1] CRAN (R 4.1.0)
 withr                    2.4.2    2021-04-18 [1] CRAN (R 4.1.0)
 xfun                     0.24     2021-06-15 [1] CRAN (R 4.1.0)
 XML                      3.99-0.6 2021-03-16 [1] CRAN (R 4.1.0)
 xml2                     1.3.2    2020-04-23 [1] CRAN (R 4.1.0)
 xtable                   1.8-4    2019-04-21 [1] CRAN (R 4.1.0)
 XVector                  0.32.0   2021-05-19 [1] Bioconductor  
 yaml                     2.2.1    2020-02-01 [1] CRAN (R 4.1.0)
 zlibbioc                 1.38.0   2021-05-19 [1] Bioconductor  

[1] /opt/R/4.1.0/lib/R/library

The output of sessioninfo::session_info() includes relevant GitHub installation information and other details that are missed by sessionInfo().

lcolladotor commented 3 years ago

Hi,

Can you provide a small reproducible example and maybe some screenshots? You could use the data from fetch_data(type = "spe") and then include a line of code that adds a column to the colData() with the data you want, plus then the code of you are telling spatialLIBD to change the default annotation and a screenshot of how it looks.

Thanks.

Best, Leo

lcolladotor commented 2 years ago

I'm closing this issue due to inactivity. Feel free to re-open it though.