Bug report: Error in data2set(X, Xcat, n_neighbors, metrics, nn_method, n_trees, search_k, : Block 1 has zero size

[JohannesGawron]

Trying to run the function scROSHI returned the error mesage in the title.

Here's the code that I ran:

scROSHI(sce_data = sce,
        celltype_lists = marker_list,
        type_config = config,
        gene_symbol = 'X',
        count_data = 'dsb_no_iso',
        verbose = 1
        )

and my singleCellExperiment object looks like this:

class: SingleCellExperiment 
dim: 45 3769 
metadata(2): libraryName assayMetadata
assays(5): counts clrc clrb dsb dsb_no_iso
rownames: NULL
rowData names(1): X
colnames: NULL
colData names(2): Sample barcodes
reducedDimNames(0):
mainExpName: NULL
altExpNames(0):

sessionInfo()
R version 4.3.1 (2023-06-16)
Platform: x86_64-apple-darwin20 (64-bit)
Running under: macOS Sonoma 14.3.1

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib;  LAPACK version 3.11.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: Europe/Zurich
tzcode source: internal

attached base packages:
[1] stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] scROSHI_1.0.0.0             umap_0.2.10.0               SingleCellExperiment_1.22.0 SummarizedExperiment_1.30.2 Biobase_2.60.0              GenomicRanges_1.52.1        GenomeInfoDb_1.36.4        
 [8] IRanges_2.34.1              S4Vectors_0.38.2            BiocGenerics_0.46.0         MatrixGenerics_1.12.3       matrixStats_1.2.0           rhdf5_2.44.0                lubridate_1.9.3            
[15] forcats_1.0.0               stringr_1.5.1               dplyr_1.1.4                 purrr_1.0.2                 readr_2.1.5                 tidyr_1.3.1                 tibble_3.2.1               
[22] ggplot2_3.5.0               tidyverse_2.0.0             Rcpp_1.0.12                

loaded via a namespace (and not attached):
  [1] RColorBrewer_1.1-3      rstudioapi_0.15.0       jsonlite_1.8.8          magrittr_2.0.3          spatstat.utils_3.0-4    farver_2.1.1            rmarkdown_2.26          zlibbioc_1.46.0         vctrs_0.6.5            
 [10] ROCR_1.0-11             spatstat.explore_3.2-6  RCurl_1.98-1.14         askpass_1.2.0           htmltools_0.5.7         S4Arrays_1.0.6          Rhdf5lib_1.22.1         sctransform_0.4.1       parallelly_1.37.1      
 [19] KernSmooth_2.23-21      htmlwidgets_1.6.4       ica_1.0-3               plyr_1.8.9              plotly_4.10.4           zoo_1.8-12              igraph_2.0.2            mime_0.12               lifecycle_1.0.4        
 [28] pkgconfig_2.0.3         Matrix_1.6-5            R6_2.5.1                fastmap_1.1.1           GenomeInfoDbData_1.2.10 fitdistrplus_1.1-11     future_1.33.1           shiny_1.8.0             digest_0.6.34          
 [37] colorspace_2.1-0        patchwork_1.2.0         tensor_1.5              Seurat_5.0.2            RSpectra_0.16-1         irlba_2.3.5.1           pkgload_1.3.4           labeling_0.4.3          progressr_0.14.0       
 [46] spatstat.sparse_3.0-3   fansi_1.0.6             timechange_0.3.0        polyclip_1.10-6         httr_1.4.7              abind_1.4-5             compiler_4.3.1          bit64_4.0.5             withr_3.0.0            
 [55] fastDummies_1.7.3       MASS_7.3-60             openssl_2.1.1           DelayedArray_0.26.7     tools_4.3.1             lmtest_0.9-40           httpuv_1.6.14           future.apply_1.11.1     goftest_1.2-3          
 [64] glue_1.7.0              nlme_3.1-162            rhdf5filters_1.12.1     promises_1.2.1          grid_4.3.1              Rtsne_0.17              reshape2_1.4.4          cluster_2.1.4           generics_0.1.3         
 [73] spatstat.data_3.0-4     gtable_0.3.4            tzdb_0.4.0              data.table_1.15.2       hms_1.1.3               sp_2.1-3                utf8_1.2.4              XVector_0.40.0          spatstat.geom_3.2-9    
 [82] RcppAnnoy_0.0.22        ggrepel_0.9.5           RANN_2.6.1              pillar_1.9.0            spam_2.10-0             RcppHNSW_0.6.0          vroom_1.6.5             limma_3.56.2            later_1.3.2            
 [91] splines_4.3.1           lattice_0.21-8          deldir_2.0-4            survival_3.5-5          FNN_1.1.4               bit_4.0.5               tidyselect_1.2.0        miniUI_0.1.1.1          pbapply_1.7-2          
[100] knitr_1.45              gridExtra_2.3           scattermore_1.2         xfun_0.42               stringi_1.8.3           lazyeval_0.2.2          yaml_2.3.8              evaluate_0.23           codetools_0.2-19       
[109] cli_3.6.2               uwot_0.1.16             xtable_1.8-4            reticulate_1.35.0       munsell_0.5.0           spatstat.random_3.2-3   globals_0.16.2          png_0.1-8               parallel_4.3.1         
[118] ellipsis_0.3.2          dotCall64_1.1-1         bitops_1.0-7            listenv_0.9.1           viridisLite_0.4.2       scales_1.3.0            ggridges_0.5.6          SeuratObject_5.0.1      leiden_0.4.3.1         
[127] crayon_1.5.2            rlang_1.1.3             cowplot_1.1.3 

[JohannesGawron]

Apparently, the input singleCellExperiment object is required to have specified dimnames and the rows should be named in the same way as the gene names used in the celltype_list. Otherwise, an empty matrix is passed to uwot::umap as X argument.

I think it would make the package more user friendly to state this explicitly somewhere in the documentation, and also to have a more verbose error output. Thanks a lot in advance for considering making adaptations.

Best,

Johannes