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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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[BUG] vis_grid_clus cannot handle logical variables #80

Closed lahuuki closed 1 month ago

lahuuki commented 2 months ago

I noticed some strange behavior in vis_grid_clus() when trying to plot logical variables such as in_tissue, the same variables plot as expected in vis_clus(). Converting the lgl to factor does not fix this.

Example in spatialDLPFC_Visium_example_subset

library("spatialLIBD")

spe <- fetch_data("spatialDLPFC_Visium_example_subset")

## works on integer data
type(spe$BayesSpace_harmony_02)
# [1] "integer"

vis_grid_clus(
    spe = spe,
    clustervar = "BayesSpace_harmony_02",
    pdf = here::here(plot_dir, "spe_DLPFC_grid-BayesSpace_harmony_02.pdf"),
    sort_clust = FALSE,
    point_size = 2
)

spe_DLPFC_grid-BayesSpace_harmony_02

Doesn't work with logical data

## convert to logical
spe$BayesSpace_harmony_02_lgl <- spe$BayesSpace_harmony_02 ==1
table(spe$BayesSpace_harmony_02)

## vis_clus works fine
png(here::here(plot_dir, "spe_DLPFC_BayesSpace_harmony_02_lgl.png"))
vis_clus(
    sampleid = "Br6432_ant",
    spe = spe,
    clustervar = "BayesSpace_harmony_02_lgl",
    point_size = 2
)
dev.off()

spe_DLPFC_BayesSpace_harmony_02_lgl

##vis grib clus returns all blank points + unuseful warning
vis_grid_clus(
    spe = spe,
    clustervar = "BayesSpace_harmony_02_lgl",
    pdf = here::here(plot_dir, "spe_DLPFC_grid-BayesSpace_harmony_02_lgl.pdf"),
    sort_clust = FALSE,
    point_size = 2
)
# Warning messages:
# 1: No shared levels found between `names(values)` of the manual scale and the data's fill values. 
# 2: No shared levels found between `names(values)` of the manual scale and the data's fill values.

spe_DLPFC_grid-BayesSpace_harmony_02_lgl

## sort_clust = TRUE throws error
vis_grid_clus(
    spe = spe,
    clustervar = "BayesSpace_harmony_02_lgl",
    pdf = here::here(plot_dir, "spe_DLPFC_grid-BayesSpace_harmony_02_lgl.pdf"),
    sort_clust = TRUE,
    point_size = 2
)

# Error in `[[<-`(`*tmp*`, clustervar, value = c(`TRUE` = 1L, `NA` = NA,  : 
#                                                    1239 elements in value to replace 12107 elements

options(width = 120)
## insert session info here
─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
 setting  value
 version  R version 4.3.3 (2024-02-29)
 os       macOS Sonoma 14.5
 system   x86_64, darwin20
 ui       RStudio
 language (EN)
 collate  en_US.UTF-8
 ctype    en_US.UTF-8
 tz       America/New_York
 date     2024-06-11
 rstudio  2024.04.1+748 Chocolate Cosmos (desktop)
 pandoc   NA

─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
 package                * version     date (UTC) lib source
 abind                    1.4-5       2016-07-21 [1] CRAN (R 4.3.0)
 AnnotationDbi            1.64.1      2023-11-03 [1] Bioconductor
 AnnotationHub            3.10.1      2024-04-05 [1] Bioconductor 3.18 (R 4.3.3)
 attempt                  0.3.1       2020-05-03 [1] CRAN (R 4.3.0)
 beachmat                 2.18.1      2024-02-14 [1] Bioconductor 3.18 (R 4.3.2)
 beeswarm                 0.4.0       2021-06-01 [1] CRAN (R 4.3.0)
 benchmarkme              1.0.8       2022-06-12 [1] CRAN (R 4.3.0)
 benchmarkmeData          1.0.4       2020-04-23 [1] CRAN (R 4.3.0)
 Biobase                * 2.62.0      2023-10-24 [1] Bioconductor
 BiocFileCache            2.10.2      2024-03-27 [1] Bioconductor 3.18 (R 4.3.3)
 BiocGenerics           * 0.48.1      2023-11-01 [1] Bioconductor
 BiocIO                   1.12.0      2023-10-24 [1] Bioconductor
 BiocManager              1.30.23     2024-05-04 [1] CRAN (R 4.3.2)
 BiocNeighbors            1.20.2      2024-01-07 [1] Bioconductor 3.18 (R 4.3.2)
 BiocParallel             1.36.0      2023-10-24 [1] Bioconductor
 BiocSingular             1.18.0      2023-10-24 [1] Bioconductor
 BiocVersion              3.18.1      2023-11-15 [1] Bioconductor
 Biostrings               2.70.3      2024-03-13 [1] Bioconductor 3.18 (R 4.3.3)
 bit                      4.0.5       2022-11-15 [1] CRAN (R 4.3.0)
 bit64                    4.0.5       2020-08-30 [1] CRAN (R 4.3.0)
 bitops                   1.0-7       2021-04-24 [1] CRAN (R 4.3.0)
 blob                     1.2.4       2023-03-17 [1] CRAN (R 4.3.0)
 bslib                    0.7.0       2024-03-29 [1] CRAN (R 4.3.2)
 cachem                   1.1.0       2024-05-16 [1] CRAN (R 4.3.3)
 cli                      3.6.2       2023-12-11 [1] CRAN (R 4.3.0)
 codetools                0.2-20      2024-03-31 [1] CRAN (R 4.3.2)
 colorout               * 1.3-0.2     2024-03-21 [1] Github (jalvesaq/colorout@c6113a2)
 colorspace               2.1-0       2023-01-23 [1] CRAN (R 4.3.0)
 config                   0.3.2       2023-08-30 [1] CRAN (R 4.3.0)
 cowplot                  1.1.3       2024-01-22 [1] CRAN (R 4.3.2)
 crayon                   1.5.2       2022-09-29 [1] CRAN (R 4.3.0)
 curl                     5.2.1       2024-03-01 [1] CRAN (R 4.3.2)
 data.table               1.15.4      2024-03-30 [1] CRAN (R 4.3.2)
 DBI                      1.2.3       2024-06-02 [1] CRAN (R 4.3.3)
 dbplyr                   2.5.0       2024-03-19 [1] CRAN (R 4.3.2)
 DelayedArray             0.28.0      2023-10-24 [1] Bioconductor
 DelayedMatrixStats       1.24.0      2023-10-24 [1] Bioconductor
 devtools               * 2.4.5       2022-10-11 [1] CRAN (R 4.3.0)
 digest                   0.6.35      2024-03-11 [1] CRAN (R 4.3.2)
 doParallel               1.0.17      2022-02-07 [1] CRAN (R 4.3.0)
 dotCall64                1.1-1       2023-11-28 [1] CRAN (R 4.3.0)
 dplyr                    1.1.4       2023-11-17 [1] CRAN (R 4.3.0)
 DT                       0.33        2024-04-04 [1] CRAN (R 4.3.2)

 edgeR                    4.0.16      2024-02-18 [1] Bioconductor 3.18 (R 4.3.2)
 ellipsis                 0.3.2       2021-04-29 [1] CRAN (R 4.3.0)
 ExperimentHub            2.10.0      2023-10-24 [1] Bioconductor
 fansi                    1.0.6       2023-12-08 [1] CRAN (R 4.3.0)
 farver                   2.1.2       2024-05-13 [1] CRAN (R 4.3.3)
 fastmap                  1.2.0       2024-05-15 [1] CRAN (R 4.3.3)
 fields                   15.2        2023-08-17 [1] CRAN (R 4.3.0)
 filelock                 1.0.3       2023-12-11 [1] CRAN (R 4.3.0)
 foreach                  1.5.2       2022-02-02 [1] CRAN (R 4.3.0)
 fs                       1.6.4       2024-04-25 [1] CRAN (R 4.3.2)
 generics                 0.1.3       2022-07-05 [1] CRAN (R 4.3.0)
 GenomeInfoDb           * 1.38.8      2024-03-15 [1] Bioconductor 3.18 (R 4.3.3)
 GenomeInfoDbData         1.2.11      2024-03-21 [1] Bioconductor
 GenomicAlignments        1.38.2      2024-01-16 [1] Bioconductor 3.18 (R 4.3.2)
 GenomicRanges          * 1.54.1      2023-10-29 [1] Bioconductor
 ggbeeswarm               0.7.2       2023-04-29 [1] CRAN (R 4.3.0)
 ggplot2                  3.5.1       2024-04-23 [1] CRAN (R 4.3.2)
 ggrepel                  0.9.5       2024-01-10 [1] CRAN (R 4.3.0)
 glue                     1.7.0       2024-01-09 [1] CRAN (R 4.3.0)
 golem                    0.4.1       2023-06-05 [1] CRAN (R 4.3.0)
 gridExtra                2.3         2017-09-09 [1] CRAN (R 4.3.0)
 gtable                   0.3.5       2024-04-22 [1] CRAN (R 4.3.2)
 here                   * 1.0.1       2020-12-13 [1] CRAN (R 4.3.0)
 htmltools                0.5.8.1     2024-04-04 [1] CRAN (R 4.3.2)
 htmlwidgets              1.6.4       2023-12-06 [1] CRAN (R 4.3.0)
 httpuv                   1.6.15      2024-03-26 [1] CRAN (R 4.3.2)
 httr                     1.4.7       2023-08-15 [1] CRAN (R 4.3.0)
 interactiveDisplayBase   1.40.0      2023-10-24 [1] Bioconductor
 IRanges                * 2.36.0      2023-10-24 [1] Bioconductor
 irlba                    2.3.5.1     2022-10-03 [1] CRAN (R 4.3.0)
 iterators                1.0.14      2022-02-05 [1] CRAN (R 4.3.0)
 jquerylib                0.1.4       2021-04-26 [1] CRAN (R 4.3.0)
 jsonlite                 1.8.8       2023-12-04 [1] CRAN (R 4.3.0)
 KEGGREST                 1.42.0      2023-10-24 [1] Bioconductor
 labeling                 0.4.3       2023-08-29 [1] CRAN (R 4.3.0)
 later                    1.3.2       2023-12-06 [1] CRAN (R 4.3.0)
 lattice                  0.22-6      2024-03-20 [1] CRAN (R 4.3.2)
 lazyeval                 0.2.2       2019-03-15 [1] CRAN (R 4.3.0)
 lifecycle                1.0.4       2023-11-07 [1] CRAN (R 4.3.0)
 limma                    3.58.1      2023-10-31 [1] Bioconductor
 lobstr                   1.1.2       2022-06-22 [1] CRAN (R 4.3.0)
 locfit                   1.5-9.9     2024-03-01 [1] CRAN (R 4.3.2)
 magick                   2.8.3       2024-02-18 [1] CRAN (R 4.3.2)
 magrittr                 2.0.3       2022-03-30 [1] CRAN (R 4.3.0)
 maps                     3.4.2       2023-12-15 [1] CRAN (R 4.3.0)
 Matrix                   1.6-5       2024-01-11 [1] CRAN (R 4.3.3)
 MatrixGenerics         * 1.14.0      2023-10-24 [1] Bioconductor
 matrixStats            * 1.3.0       2024-04-11 [1] CRAN (R 4.3.2)
 memoise                  2.0.1       2021-11-26 [1] CRAN (R 4.3.0)
 mime                     0.12        2021-09-28 [1] CRAN (R 4.3.0)
 miniUI                   0.1.1.1     2018-05-18 [1] CRAN (R 4.3.0)
 munsell                  0.5.1       2024-04-01 [1] CRAN (R 4.3.2)
 paletteer                1.6.0       2024-01-21 [1] CRAN (R 4.3.0)
 pillar                   1.9.0       2023-03-22 [1] CRAN (R 4.3.0)
 pkgbuild                 1.4.4       2024-03-17 [1] CRAN (R 4.3.2)
 pkgconfig                2.0.3       2019-09-22 [1] CRAN (R 4.3.0)
 pkgload                  1.3.4       2024-01-16 [1] CRAN (R 4.3.0)
 plotly                   4.10.4      2024-01-13 [1] CRAN (R 4.3.0)
 png                      0.1-8       2022-11-29 [1] CRAN (R 4.3.0)
 profvis                  0.3.8       2023-05-02 [1] CRAN (R 4.3.0)
 promises                 1.3.0       2024-04-05 [1] CRAN (R 4.3.2)
 purrr                    1.0.2       2023-08-10 [1] CRAN (R 4.3.0)
 R6                       2.5.1       2021-08-19 [1] CRAN (R 4.3.0)
 rappdirs                 0.3.3       2021-01-31 [1] CRAN (R 4.3.0)
 RColorBrewer             1.1-3       2022-04-03 [1] CRAN (R 4.3.0)
 Rcpp                     1.0.12      2024-01-09 [1] CRAN (R 4.3.0)
 RCurl                    1.98-1.14   2024-01-09 [1] CRAN (R 4.3.0)
 rematch2                 2.1.2       2020-05-01 [1] CRAN (R 4.3.0)
 remotes                  2.5.0       2024-03-17 [1] CRAN (R 4.3.2)
 restfulr                 0.0.15      2022-06-16 [1] CRAN (R 4.3.0)
 rjson                    0.2.21      2022-01-09 [1] CRAN (R 4.3.0)
 rlang                    1.1.4       2024-06-04 [1] CRAN (R 4.3.3)
 rprojroot                2.0.4       2023-11-05 [1] CRAN (R 4.3.0)
 Rsamtools                2.18.0      2023-10-24 [1] Bioconductor
 RSQLite                  2.3.7       2024-05-27 [1] CRAN (R 4.3.3)
 rstudioapi               0.16.0      2024-03-24 [1] CRAN (R 4.3.2)
 rsvd                     1.0.5       2021-04-16 [1] CRAN (R 4.3.0)
 rtracklayer              1.62.0      2023-10-24 [1] Bioconductor
 S4Arrays                 1.2.1       2024-03-06 [1] Bioconductor 3.18 (R 4.3.3)
 S4Vectors              * 0.40.2      2023-11-23 [1] Bioconductor
 sass                     0.4.9       2024-03-15 [1] CRAN (R 4.3.2)
 ScaledMatrix             1.10.0      2023-10-24 [1] Bioconductor
 scales                   1.3.0       2023-11-28 [1] CRAN (R 4.3.0)
 scater                   1.30.1      2023-12-06 [1] Bioconductor
 scuttle                  1.12.0      2023-10-24 [1] Bioconductor
 sessioninfo              1.2.2       2021-12-06 [1] CRAN (R 4.3.0)
 shiny                    1.8.1.1     2024-04-02 [1] CRAN (R 4.3.2)
 shinyWidgets             0.8.6       2024-04-24 [1] CRAN (R 4.3.2)
 SingleCellExperiment   * 1.24.0      2023-10-24 [1] Bioconductor
 spam                     2.10-0      2023-10-23 [1] CRAN (R 4.3.0)
 SparseArray              1.2.4       2024-02-11 [1] Bioconductor 3.18 (R 4.3.2)
 sparseMatrixStats        1.14.0      2023-10-24 [1] Bioconductor
 SpatialExperiment      * 1.12.0      2023-10-24 [1] Bioconductor
 spatialLIBD            * 1.17.2      2024-06-06 [1] Github (LieberInstitute/spatialLIBD@e0947a2)
 statmod                  1.5.0       2023-01-06 [1] CRAN (R 4.3.0)
 stringi                  1.8.4       2024-05-06 [1] CRAN (R 4.3.2)
 stringr                  1.5.1       2023-11-14 [1] CRAN (R 4.3.0)
 SummarizedExperiment   * 1.32.0      2023-10-24 [1] Bioconductor
 tibble                   3.2.1       2023-03-20 [1] CRAN (R 4.3.0)
 tidyr                    1.3.1       2024-01-24 [1] CRAN (R 4.3.2)
 tidyselect               1.2.1       2024-03-11 [1] CRAN (R 4.3.2)
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 usethis                * 2.2.3       2024-02-19 [1] CRAN (R 4.3.2)
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 withr                    3.0.0       2024-01-16 [1] CRAN (R 4.3.0)
 XML                      3.99-0.16.1 2024-01-22 [1] CRAN (R 4.3.2)
 xtable                   1.8-4       2019-04-21 [1] CRAN (R 4.3.0)
 XVector                  0.42.0      2023-10-24 [1] Bioconductor
 yaml                     2.3.8       2023-12-11 [1] CRAN (R 4.3.0)
 zlibbioc                 1.48.2      2024-03-13 [1] Bioconductor 3.18 (R 4.3.3)

 [1] /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library

Note. spatialLIBD is a recent github version

Additional Context

I found this bug plotting data from the LFF_spatial_ERC project: more examples of this issue

Is the package installed via bioconda? No

lcolladotor commented 1 month ago

Thanks for the report @lahuuki!

Here's how things behave now in spatialLIBD version 1.17.6. See https://github.com/LieberInstitute/spatialLIBD/commit/08c2b2d80a29b1decee578d01f7230b595a9bf5a for more details on the internal changes to sort_clusters() and get_colors().

Best, Leo

suppressPackageStartupMessages(library("spatialLIBD"))
spe <- fetch_data("spatialDLPFC_Visium_example_subset")
#> 2024-07-12 10:58:34.14279 loading file /Users/leocollado/Library/Caches/org.R-project.R/R/BiocFileCache/6f563a40ecf7_spatialDLPFC_spe_subset_example.rds%3Fdl%3D1
spe$BayesSpace_harmony_02_lgl <- spe$BayesSpace_harmony_02 ==1
set.seed(20240712)
spe$BayesSpace_harmony_02_lgl[sample(seq_len(ncol(spe)), 2000)] <- NA

vis_grid_clus(
    spe = spe,
    clustervar = "BayesSpace_harmony_02_lgl",
    return_plots = TRUE,
    sort_clust = FALSE,
    point_size = 2
)
#> $Br6432_ant

#> 
#> $Br6522_ant

#> 
#> $Br8667_mid


vis_grid_clus(
    spe = spe,
    clustervar = "BayesSpace_harmony_02_lgl",
    return_plots = TRUE,
    sort_clust = TRUE,
    point_size = 2
)
#> $Br6432_ant

#> 
#> $Br6522_ant

#> 
#> $Br8667_mid


vis_clus(
    sampleid = "Br6432_ant",
    spe = spe,
    clustervar = "BayesSpace_harmony_02_lgl",
    point_size = 2
)


packageVersion("spatialLIBD")
#> [1] '1.17.6'

Created on 2024-07-12 with reprex v2.1.0