Hi,

I am trying to load my graph based annotations into the interactive shiny app. I denote my own annotations as default but they do not show up on the map. I think the original data's (from the spatialLIBD) are still called.

run_app(
  spe,
  sce_layer = NULL,
  modeling_results = NULL,
  sig_genes = NULL,
  title = "Mouse Visium",
  docs_path = "./www",
  spe_discrete_vars = c("annotations","ManualAnnotation"),
  spe_continuous_vars = c("sum_umi", "sum_gene", "expr_chrM", "expr_chrM_ratio"),
  default_cluster = "annotations"
)



sessionInfo( )

─ 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) farver 2.1.0 2021-02-28 [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) labeling 0.4.2 2020-10-20 [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
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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