VariableFeaturePlot produced "incorrect number of dimensions" error for merged SCTransform-ed objects

[denvercal1234GitHub]

Related to the bugs in #4018 and #6412, VariableFeaturePlot() produced "incorrect number of dimensions" error for merged SCTransform-ed objects.

Would you mind advising us how to proceed to obtain the info for and visualize the variable features after we use SelectIntegrationFeatures() to select the variable features for the merged Seurat obj?

Thank you.

VariableFeaturePlot(merged_obj, assay = "SCT", selection.method = "sct")

Error:

Error in SCTResults(object = object, slot = "feature.attributes")[, vars] :
incorrect number of dimensions

> sessionInfo()
R version 4.2.0 (2022-04-22)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS:   /Filers/package/R-base/4.2.0/lib64/R/lib/libRblas.so
LAPACK: /Filers/package/R-base/4.2.0/lib64/R/lib/libRlapack.so

locale:
 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C               LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8     LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8    LC_PAPER=en_GB.UTF-8      
 [8] LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] ggplot2_3.3.6      dplyr_1.0.10       sp_1.5-0           SeuratObject_4.1.0 Seurat_4.1.1       reticulate_1.25    knitr_1.39        

loaded via a namespace (and not attached):
  [1] utf8_1.2.2                  R.utils_2.11.0              ks_1.13.5                   tidyselect_1.1.2            htmlwidgets_1.5.4           grid_4.2.0                  BiocParallel_1.30.3        
  [8] Rtsne_0.16                  devtools_2.4.3              munsell_0.5.0               ScaledMatrix_1.4.0          codetools_0.2-18            ica_1.0-2                   future_1.26.1              
 [15] miniUI_0.1.1.1              withr_2.5.0                 spatstat.random_2.2-0       colorspace_2.0-3            progressr_0.10.1            Biobase_2.56.0              rstudioapi_0.13            
 [22] stats4_4.2.0                SingleCellExperiment_1.18.0 ROCR_1.0-11                 pastecs_1.3.21              tensor_1.5                  listenv_0.8.0               labeling_0.4.2             
 [29] MatrixGenerics_1.8.1        GenomeInfoDbData_1.2.8      polyclip_1.10-0             farver_2.1.1                Nebulosa_1.6.0              parallelly_1.32.0           vctrs_0.4.1                
 [36] generics_0.1.3              xfun_0.30                   R6_2.5.1                    GenomeInfoDb_1.32.3         ggbeeswarm_0.6.0            rsvd_1.0.5                  locfit_1.5-9.5             
 [43] flexmix_2.3-18              bitops_1.0-7                spatstat.utils_2.3-1        cachem_1.0.6                DelayedArray_0.22.0         assertthat_0.2.1            promises_1.2.0.1           
 [50] scales_1.2.1                nnet_7.3-17                 rgeos_0.5-9                 beeswarm_0.4.0              gtable_0.3.1                beachmat_2.12.0             globals_0.15.0             
 [57] processx_3.7.0              goftest_1.2-3               rlang_1.0.5                 splines_4.2.0               lazyeval_0.2.2              spatstat.geom_2.4-0         yaml_2.3.5                 
 [64] BiocManager_1.30.18         reshape2_1.4.4              abind_1.4-5                 httpuv_1.6.5                gridtext_0.1.4              usethis_2.1.6               tools_4.2.0                
 [71] ellipsis_0.3.2              spatstat.core_2.4-4         jquerylib_0.1.4             RColorBrewer_1.1-3          BiocGenerics_0.42.0         sessioninfo_1.2.2           ggridges_0.5.3             
 [78] Rcpp_1.0.9                  plyr_1.8.7                  sparseMatrixStats_1.8.0     zlibbioc_1.42.0             purrr_0.3.4                 RCurl_1.98-1.8              prettyunits_1.1.1          
 [85] ps_1.7.1                    rpart_4.1.16                deldir_1.0-6                pbapply_1.5-0               viridis_0.6.2               cowplot_1.1.1               S4Vectors_0.34.0           
 [92] zoo_1.8-10                  SummarizedExperiment_1.26.1 ggrepel_0.9.1               cluster_2.1.3               fs_1.5.2                    magrittr_2.0.3              glmGamPoi_1.8.0            
 [99] RSpectra_0.16-1             data.table_1.14.2           scattermore_0.8             lmtest_0.9-40               RANN_2.6.1                  mvtnorm_1.1-3               fitdistrplus_1.1-8         
[106] matrixStats_0.62.0          pkgload_1.3.0               evaluate_0.15               patchwork_1.1.1             mime_0.12                   xtable_1.8-4                mclust_5.4.10              
[113] IRanges_2.30.1              gridExtra_2.3               compiler_4.2.0              scater_1.24.0               tibble_3.1.8                crayon_1.5.1                KernSmooth_2.23-20         
[120] R.oo_1.24.0                 htmltools_0.5.2             mgcv_1.8-40                 later_1.3.0                 tidyr_1.2.0                 ggtext_0.1.1                DBI_1.1.3                  
[127] MASS_7.3-57                 boot_1.3-28                 Matrix_1.4-1                cli_3.3.0                   R.methodsS3_1.8.1           parallel_4.2.0              igraph_1.3.4               
[134] GenomicRanges_1.48.0        pkgconfig_2.0.3             plotly_4.10.0               scuttle_1.6.2               spatstat.sparse_2.1-1       xml2_1.3.3                  bslib_0.4.0                
[141] vipor_0.4.5                 XVector_0.36.0              stringr_1.4.1               callr_3.7.0                 digest_0.6.29               sctransform_0.3.3           RcppAnnoy_0.0.19           
[148] pracma_2.3.8                spatstat.data_2.2-0         rmarkdown_2.14              leiden_0.4.2                uwot_0.1.11                 edgeR_3.38.1                DelayedMatrixStats_1.18.0  
[155] shiny_1.7.1                 modeltools_0.2-23           lifecycle_1.0.1             nlme_3.1-157                jsonlite_1.8.0              SeuratWrappers_0.3.0        BiocNeighbors_1.14.0       
[162] viridisLite_0.4.1           limma_3.52.1                fansi_1.0.3                 pillar_1.8.1                lattice_0.20-45             ggrastr_1.0.1               fastmap_1.1.0              
[169] httr_1.4.4                  pkgbuild_1.3.1              survival_3.3-1              glue_1.6.2                  remotes_2.4.2               png_0.1-7                   sass_0.4.1                 
[176] stringi_1.7.8               BiocSingular_1.12.0         memoise_2.0.1               irlba_2.3.5                 future.apply_1.9.0