[BUG/Question] What's the layer annotation variable in the spe object?

sluan-jh commented 1 month ago

Hello,

Since fetch_data returns error on my machine, I manually downloaded data from the https link for type == "sce" in the fetch_data() function and converted the downloaded sce to spe using sce_to_spe().

>fetch_data(type = "spe")
snapshotDate(): 2024-04-29
Error in inherits(ram, "try-error") || length(ram) == 0L || is.na(ram) : 
  'length = 3' in coercion to 'logical(1)'

When I try to replicate the example code below:

vis_clus(
    spe = spe,
    clustervar = "spatialLIBD",
    sampleid = "151673",
    colors = libd_layer_colors,
    ... = " DLPFC Human Brain Layers\nMade with research.libd.org/spatialLIBD/"
)

I couldn't find a variable named "spatialLIBD" in the colData, but it seems using the column "layer_guess_reordered_short" produces the same result.

Is "layer_guess_reordered_short" the annotation of the layers?

Session info is attached below in case it's helpful

> options(width = 120)
> sessioninfo::session_info()
─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
 setting  value
 version  R version 4.4.1 (2024-06-14 ucrt)
 os       Windows 10 x64 (build 19045)
 system   x86_64, mingw32
 ui       RStudio
 language (EN)
 collate  English_United States.utf8
 ctype    English_United States.utf8
 tz       America/New_York
 date     2024-10-15
 rstudio  2024.04.2+764 Chocolate Cosmos (desktop)
 pandoc   NA

─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
 package              * version   date (UTC) lib source
 abind                  1.4-8     2024-09-12 [1] CRAN (R 4.4.1)
 AnnotationDbi          1.66.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 AnnotationHub          3.12.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 attempt                0.3.1     2020-05-03 [1] CRAN (R 4.4.1)
 basilisk             * 1.16.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 basilisk.utils         1.16.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 beachmat               2.20.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 beeswarm               0.4.0     2021-06-01 [1] CRAN (R 4.4.0)
 benchmarkme            1.0.8     2022-06-12 [1] CRAN (R 4.4.1)
 benchmarkmeData        1.0.4     2020-04-23 [1] CRAN (R 4.4.1)
 Biobase              * 2.64.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 BiocFileCache        * 2.12.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 BiocGenerics         * 0.50.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 BiocIO                 1.14.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 BiocManager            1.30.25   2024-08-28 [1] CRAN (R 4.4.1)
 BiocNeighbors          1.22.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 BiocParallel           1.38.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 BiocSingular           1.20.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 BiocVersion            3.19.1    2024-04-17 [1] Bioconductor 3.19 (R 4.4.0)
 Biostrings             2.72.1    2024-06-02 [1] Bioconductor 3.19 (R 4.4.0)
 bit                    4.0.5     2022-11-15 [1] CRAN (R 4.4.1)
 bit64                  4.0.5     2020-08-30 [1] CRAN (R 4.4.1)
 bitops                 1.0-9     2024-10-03 [1] CRAN (R 4.4.1)
 blob                   1.2.4     2023-03-17 [1] CRAN (R 4.4.1)
 bslib                  0.8.0     2024-07-29 [1] CRAN (R 4.4.1)
 cachem                 1.1.0     2024-05-16 [1] CRAN (R 4.4.1)
 cli                    3.6.3     2024-06-21 [1] CRAN (R 4.4.1)
 codetools              0.2-20    2024-03-31 [2] CRAN (R 4.4.1)
 colorspace             2.1-1     2024-07-26 [1] CRAN (R 4.4.1)
 config                 0.3.2     2023-08-30 [1] CRAN (R 4.4.1)
 cowplot                1.1.3     2024-01-22 [1] CRAN (R 4.4.1)
 crayon                 1.5.3     2024-06-20 [1] CRAN (R 4.4.1)
 curl                   5.2.2     2024-08-26 [1] CRAN (R 4.4.1)
 data.table             1.16.0    2024-08-27 [1] CRAN (R 4.4.1)
 DBI                    1.2.3     2024-06-02 [1] CRAN (R 4.4.1)
 dbplyr               * 2.5.0     2024-03-19 [1] CRAN (R 4.4.1)
 DelayedArray           0.30.1    2024-05-08 [1] Bioconductor 3.19 (R 4.4.0)
 DelayedMatrixStats     1.26.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 digest                 0.6.37    2024-08-19 [1] CRAN (R 4.4.1)
 dir.expiry             1.12.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 doParallel             1.0.17    2022-02-07 [1] CRAN (R 4.4.1)
 dotCall64              1.2       2024-10-04 [1] CRAN (R 4.4.1)
 dplyr                  1.1.4     2023-11-17 [1] CRAN (R 4.4.1)
 DT                     0.33      2024-04-04 [1] CRAN (R 4.4.1)
 edgeR                  4.2.1     2024-07-21 [1] Bioconductor 3.19 (R 4.4.1)
 ExperimentHub          2.12.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 fansi                  1.0.6     2023-12-08 [1] CRAN (R 4.4.1)
 fastmap                1.2.0     2024-05-15 [1] CRAN (R 4.4.1)
 fields                 16.3      2024-09-30 [1] CRAN (R 4.4.1)
 filelock               1.0.3     2023-12-11 [1] CRAN (R 4.4.1)
 foreach                1.5.2     2022-02-02 [1] CRAN (R 4.4.1)
 generics               0.1.3     2022-07-05 [1] CRAN (R 4.4.1)
 GenomeInfoDb         * 1.40.1    2024-06-16 [1] Bioconductor 3.19 (R 4.4.0)
 GenomeInfoDbData       1.2.12    2024-10-10 [1] Bioconductor
 GenomicAlignments      1.40.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 GenomicRanges        * 1.56.1    2024-06-12 [1] Bioconductor 3.19 (R 4.4.0)
 ggbeeswarm             0.7.2     2023-04-29 [1] CRAN (R 4.4.1)
 ggplot2                3.5.1     2024-04-23 [1] CRAN (R 4.4.1)
 ggrepel                0.9.6     2024-09-07 [1] CRAN (R 4.4.1)
 glue                   1.7.0     2024-01-09 [1] CRAN (R 4.4.1)
 golem                  0.5.1     2024-08-27 [1] CRAN (R 4.4.1)
 gridExtra              2.3       2017-09-09 [1] CRAN (R 4.4.1)
 gtable                 0.3.5     2024-04-22 [1] CRAN (R 4.4.1)
 hms                    1.1.3     2023-03-21 [1] CRAN (R 4.4.1)
 htmltools              0.5.8.1   2024-04-04 [1] CRAN (R 4.4.1)
 htmlwidgets            1.6.4     2023-12-06 [1] CRAN (R 4.4.1)
 httpuv                 1.6.15    2024-03-26 [1] CRAN (R 4.4.1)
 httr                   1.4.7     2023-08-15 [1] CRAN (R 4.4.1)
 IRanges              * 2.38.1    2024-07-03 [1] Bioconductor 3.19 (R 4.4.1)
 irlba                  2.3.5.1   2022-10-03 [1] CRAN (R 4.4.1)
 iterators              1.0.14    2022-02-05 [1] CRAN (R 4.4.1)
 jquerylib              0.1.4     2021-04-26 [1] CRAN (R 4.4.1)
 jsonlite               1.8.8     2023-12-04 [1] CRAN (R 4.4.1)
 KEGGREST               1.44.1    2024-06-19 [1] Bioconductor 3.19 (R 4.4.0)
 later                  1.3.2     2023-12-06 [1] CRAN (R 4.4.1)
 lattice                0.22-6    2024-03-20 [2] CRAN (R 4.4.1)
 lazyeval               0.2.2     2019-03-15 [1] CRAN (R 4.4.1)
 lifecycle              1.0.4     2023-11-07 [1] CRAN (R 4.4.1)
 limma                  3.60.6    2024-10-02 [1] Bioconductor 3.19 (R 4.4.1)
 lobstr               * 1.1.2     2022-06-22 [1] CRAN (R 4.4.1)
 locfit                 1.5-9.10  2024-06-24 [1] CRAN (R 4.4.1)
 magick                 2.8.5     2024-09-20 [1] CRAN (R 4.4.1)
 magrittr               2.0.3     2022-03-30 [1] CRAN (R 4.4.1)
 maps                   3.4.2     2023-12-15 [1] CRAN (R 4.4.1)
 Matrix               * 1.7-0     2024-04-26 [2] CRAN (R 4.4.1)
 MatrixGenerics       * 1.16.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 matrixStats          * 1.4.1     2024-09-08 [1] CRAN (R 4.4.1)
 memoise                2.0.1     2021-11-26 [1] CRAN (R 4.4.1)
 mime                   0.12      2021-09-28 [1] CRAN (R 4.4.0)
 munsell                0.5.1     2024-04-01 [1] CRAN (R 4.4.1)
 paletteer              1.6.0     2024-01-21 [1] CRAN (R 4.4.1)
 pillar                 1.9.0     2023-03-22 [1] CRAN (R 4.4.1)
 pkgconfig              2.0.3     2019-09-22 [1] CRAN (R 4.4.1)
 plotly                 4.10.4    2024-01-13 [1] CRAN (R 4.4.1)
 png                    0.1-8     2022-11-29 [1] CRAN (R 4.4.0)
 promises               1.3.0     2024-04-05 [1] CRAN (R 4.4.1)
 purrr                  1.0.2     2023-08-10 [1] CRAN (R 4.4.1)
 R6                     2.5.1     2021-08-19 [1] CRAN (R 4.4.1)
 rappdirs               0.3.3     2021-01-31 [1] CRAN (R 4.4.1)
 raster               * 3.6-26    2023-10-14 [1] CRAN (R 4.4.1)
 RColorBrewer           1.1-3     2022-04-03 [1] CRAN (R 4.4.0)
 Rcpp                   1.0.13    2024-07-17 [1] CRAN (R 4.4.1)
 RCurl                  1.98-1.16 2024-07-11 [1] CRAN (R 4.4.1)
 readr                * 2.1.5     2024-01-10 [1] CRAN (R 4.4.1)
 rematch2               2.1.2     2020-05-01 [1] CRAN (R 4.4.1)
 restfulr               0.0.15    2022-06-16 [1] CRAN (R 4.4.1)
 reticulate           * 1.39.0    2024-09-05 [1] CRAN (R 4.4.1)
 rjson                  0.2.23    2024-09-16 [1] CRAN (R 4.4.1)
 rlang                  1.1.4     2024-06-04 [1] CRAN (R 4.4.1)
 Rsamtools              2.20.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 RSQLite                2.3.7     2024-05-27 [1] CRAN (R 4.4.1)
 rstudioapi             0.16.0    2024-03-24 [1] CRAN (R 4.4.1)
 rsvd                   1.0.5     2021-04-16 [1] CRAN (R 4.4.1)
 rtracklayer            1.64.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 S4Arrays               1.4.1     2024-05-20 [1] Bioconductor 3.19 (R 4.4.0)
 S4Vectors            * 0.42.1    2024-07-03 [1] Bioconductor 3.19 (R 4.4.1)
 sass                   0.4.9     2024-03-15 [1] CRAN (R 4.4.1)
 ScaledMatrix           1.12.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 scales                 1.3.0     2023-11-28 [1] CRAN (R 4.4.1)
 scater                 1.32.1    2024-07-21 [1] Bioconductor 3.19 (R 4.4.1)
 scuttle                1.14.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 sessioninfo            1.2.2     2021-12-06 [1] CRAN (R 4.4.1)
 shiny                  1.9.1     2024-08-01 [1] CRAN (R 4.4.1)
 shinyWidgets           0.8.7     2024-09-23 [1] CRAN (R 4.4.1)
 SingleCellExperiment * 1.26.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 sp                   * 2.1-4     2024-04-30 [1] CRAN (R 4.4.1)
 spam                   2.11-0    2024-10-03 [1] CRAN (R 4.4.1)
 SparseArray            1.4.8     2024-06-02 [1] Bioconductor 3.19 (R 4.4.0)
 sparseMatrixStats      1.16.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 SpatialExperiment    * 1.14.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 spatialLIBD          * 1.16.2    2024-05-28 [1] Bioconductor 3.19 (R 4.4.1)
 statmod                1.5.0     2023-01-06 [1] CRAN (R 4.4.1)
 SummarizedExperiment * 1.34.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 terra                  1.7-78    2024-05-22 [1] CRAN (R 4.4.1)
 tibble                 3.2.1     2023-03-20 [1] CRAN (R 4.4.1)
 tidyr                  1.3.1     2024-01-24 [1] CRAN (R 4.4.1)
 tidyselect             1.2.1     2024-03-11 [1] CRAN (R 4.4.1)
 tzdb                   0.4.0     2023-05-12 [1] CRAN (R 4.4.1)
 UCSC.utils             1.0.0     2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 utf8                   1.2.4     2023-10-22 [1] CRAN (R 4.4.1)
 vctrs                  0.6.5     2023-12-01 [1] CRAN (R 4.4.1)
 vipor                  0.4.7     2023-12-18 [1] CRAN (R 4.4.1)
 viridis                0.6.5     2024-01-29 [1] CRAN (R 4.4.1)
 viridisLite            0.4.2     2023-05-02 [1] CRAN (R 4.4.1)
 withr                  3.0.1     2024-07-31 [1] CRAN (R 4.4.1)
 XML                    3.99-0.17 2024-06-25 [1] CRAN (R 4.4.1)
 xtable                 1.8-4     2019-04-21 [1] CRAN (R 4.4.1)
 XVector                0.44.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 yaml                   2.3.10    2024-07-26 [1] CRAN (R 4.4.1)
 zellkonverter        * 1.14.1    2024-06-26 [1] Bioconductor 3.19 (R 4.4.0)
 zlibbioc               1.50.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)

 [1] C:/Users/Shu Luan/AppData/Local/R/win-library/4.4
 [2] C:/Program Files/R/R-4.4.1/library

──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────

Thank you!

lcolladotor commented 1 month ago

Hi,

Since you are not using fetch_data() you are missing these internal steps https://github.com/LieberInstitute/spatialLIBD/blob/c82c789d8538fe52e90d33af852a92d23b2368c4/R/fetch_data.R#L336-L345.

I haven't heard of this error before and would need more information, like the output of traceback().

Error in inherits(ram, "try-error") || length(ram) == 0L || is.na(ram) : 
  'length = 3' in coercion to 'logical(1)'

Maybe it's an issue with Windows 10 x64 but well, I'm not sure.

Best, Leo

sluan-jh commented 1 month ago

Hi Leo,

That makes sense now. Thank you!

For the bug, here's the traceback:

> fetch_data(type = "spe")
snapshotDate(): 2024-04-29
Error in inherits(ram, "try-error") || length(ram) == 0L || is.na(ram) : 
  'length = 3' in coercion to 'logical(1)'
> traceback()
8: get_ram()
7: enough_ram()
6: fetch_data("sce", destdir = destdir, eh = eh)
5: is(sce, "SingleCellExperiment")
4: stopifnot(is(sce, "SingleCellExperiment"))
3: check_sce(sce)
2: sce_to_spe(fetch_data("sce", destdir = destdir, eh = eh))
1: fetch_data(type = "spe")

Best, Shu

lcolladotor commented 1 month ago

I see, looks like https://github.com/LieberInstitute/spatialLIBD/blob/c82c789d8538fe52e90d33af852a92d23b2368c4/R/enough_ram.R#L23 is failing for you. It's from https://github.com/LieberInstitute/spatialLIBD/blob/c82c789d8538fe52e90d33af852a92d23b2368c4/R/enough_ram.R#L12.

What is the output of the following for you?

## Reproduce error
benchmarkme::get_ram()
traceback()

## R Session info
options(width = 120)
sessioninfo::session_info()

It might be worth reporting the output of this at https://github.com/csgillespie/benchmarkme. Looks like https://github.com/csgillespie/benchmarkme/issues/49 might be related, which coincidentally (aka suspicious now) was also reported by a Windows 10 user.

Best, Leo

sluan-jh commented 1 month ago

Hi Leo,

This is the output of the code you provided.

> ## Reproduce error
> benchmarkme::get_ram()
Error in inherits(ram, "try-error") || length(ram) == 0L || is.na(ram) : 
  'length = 3' in coercion to 'logical(1)'
> traceback()
1: benchmarkme::get_ram()
> ## R Session info
> options(width = 120)
> sessioninfo::session_info()
─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
 setting  value
 version  R version 4.4.1 (2024-06-14 ucrt)
 os       Windows 10 x64 (build 19045)
 system   x86_64, mingw32
 ui       RStudio
 language (EN)
 collate  English_United States.utf8
 ctype    English_United States.utf8
 tz       America/New_York
 date     2024-10-15
 rstudio  2024.04.2+764 Chocolate Cosmos (desktop)
 pandoc   NA

─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
 package              * version   date (UTC) lib source
 abind                  1.4-8     2024-09-12 [1] CRAN (R 4.4.1)
 AnnotationDbi          1.66.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 AnnotationHub          3.12.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 attempt                0.3.1     2020-05-03 [1] CRAN (R 4.4.1)
 basilisk             * 1.16.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 basilisk.utils         1.16.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 beachmat               2.20.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 beeswarm               0.4.0     2021-06-01 [1] CRAN (R 4.4.0)
 benchmarkme            1.0.8     2022-06-12 [1] CRAN (R 4.4.1)
 benchmarkmeData        1.0.4     2020-04-23 [1] CRAN (R 4.4.1)
 Biobase              * 2.64.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 BiocFileCache        * 2.12.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 BiocGenerics         * 0.50.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 BiocIO                 1.14.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 BiocManager            1.30.25   2024-08-28 [1] CRAN (R 4.4.1)
 BiocNeighbors          1.22.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 BiocParallel           1.38.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 BiocSingular           1.20.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 BiocVersion            3.19.1    2024-04-17 [1] Bioconductor 3.19 (R 4.4.0)
 Biostrings             2.72.1    2024-06-02 [1] Bioconductor 3.19 (R 4.4.0)
 bit                    4.0.5     2022-11-15 [1] CRAN (R 4.4.1)
 bit64                  4.0.5     2020-08-30 [1] CRAN (R 4.4.1)
 bitops                 1.0-9     2024-10-03 [1] CRAN (R 4.4.1)
 blob                   1.2.4     2023-03-17 [1] CRAN (R 4.4.1)
 bslib                  0.8.0     2024-07-29 [1] CRAN (R 4.4.1)
 cachem                 1.1.0     2024-05-16 [1] CRAN (R 4.4.1)
 cli                    3.6.3     2024-06-21 [1] CRAN (R 4.4.1)
 codetools              0.2-20    2024-03-31 [2] CRAN (R 4.4.1)
 colorspace             2.1-1     2024-07-26 [1] CRAN (R 4.4.1)
 config                 0.3.2     2023-08-30 [1] CRAN (R 4.4.1)
 cowplot                1.1.3     2024-01-22 [1] CRAN (R 4.4.1)
 crayon                 1.5.3     2024-06-20 [1] CRAN (R 4.4.1)
 curl                   5.2.2     2024-08-26 [1] CRAN (R 4.4.1)
 data.table             1.16.0    2024-08-27 [1] CRAN (R 4.4.1)
 DBI                    1.2.3     2024-06-02 [1] CRAN (R 4.4.1)
 dbplyr               * 2.5.0     2024-03-19 [1] CRAN (R 4.4.1)
 DelayedArray           0.30.1    2024-05-08 [1] Bioconductor 3.19 (R 4.4.0)
 DelayedMatrixStats     1.26.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 digest                 0.6.37    2024-08-19 [1] CRAN (R 4.4.1)
 dir.expiry             1.12.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 doParallel             1.0.17    2022-02-07 [1] CRAN (R 4.4.1)
 dotCall64              1.2       2024-10-04 [1] CRAN (R 4.4.1)
 dplyr                  1.1.4     2023-11-17 [1] CRAN (R 4.4.1)
 DT                     0.33      2024-04-04 [1] CRAN (R 4.4.1)
 edgeR                  4.2.1     2024-07-21 [1] Bioconductor 3.19 (R 4.4.1)
 ExperimentHub          2.12.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 fansi                  1.0.6     2023-12-08 [1] CRAN (R 4.4.1)
 fastmap                1.2.0     2024-05-15 [1] CRAN (R 4.4.1)
 fields                 16.3      2024-09-30 [1] CRAN (R 4.4.1)
 filelock               1.0.3     2023-12-11 [1] CRAN (R 4.4.1)
 foreach                1.5.2     2022-02-02 [1] CRAN (R 4.4.1)
 generics               0.1.3     2022-07-05 [1] CRAN (R 4.4.1)
 GenomeInfoDb         * 1.40.1    2024-06-16 [1] Bioconductor 3.19 (R 4.4.0)
 GenomeInfoDbData       1.2.12    2024-10-10 [1] Bioconductor
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 [1] C:/Users/Shu Luan/AppData/Local/R/win-library/4.4
 [2] C:/Program Files/R/R-4.4.1/library

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lcolladotor commented 1 month ago

Thanks @sluan-jh! Well, we now need to wait for a response about https://github.com/csgillespie/benchmarkme/issues/49.

LieberInstitute / spatialLIBD

[BUG/Question] What's the layer annotation variable in the spe object? #89