search

ImmuneDynamics / Spectre

A computational toolkit in R for the integration, exploration, and analysis of high-dimensional single-cell cytometry and imaging data.
https://immunedynamics.github.io/spectre/
MIT License
56 stars 21 forks source link

Error in is(d, "matrix") : object 'dat.bk' not found during Spectre::run.umap #155

Closed denvercal1234GitHub closed 1 year ago

denvercal1234GitHub commented 1 year ago

Hi there,

Thanks for the package.

I encountered the error above while running Spectre::run.umap after I successfully ran Spectre::do.subsample.

Running sample data encountered the same error:

cell.dat <- do.subsample(Spectre::demo.asinh, 10000) # Subsample the demo dataset to 10000 cells
cell.dat <- Spectre::run.umap(
  dat = cell.dat,
  use.cols = names(demo.asinh)[c(2:10)]
)

Would you mind helping me diagnose the issue?

Thank you. 

> sessionInfo()
R version 4.2.3 (2023-03-15)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Ventura 13.3.1

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib

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

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

other attached packages:
 [1] umap_0.2.10.0        FlowSOM_2.6.0        igraph_1.4.2         Biobase_2.58.0       BiocGenerics_0.44.0  Spectre_1.0.0-0      RColorBrewer_1.1-3  
 [8] ggthemes_4.2.4       colorRamps_2.3.1     scales_1.2.1         flowVS_1.30.0        flowStats_4.10.0     flowViz_1.62.0       lattice_0.21-8      
[15] data.table_1.14.8    tensorflow_2.11.0    keras_2.11.1         gridExtra_2.3        ggcyto_1.26.4        ncdfFlow_2.44.0      BH_1.81.0-1         
[22] flowClust_3.36.1     lubridate_1.9.2      forcats_1.0.0        stringr_1.5.0        dplyr_1.1.1          purrr_1.0.1          readr_2.1.4         
[29] tidyr_1.3.0          tibble_3.2.1         ggplot2_3.4.2        tidyverse_2.0.0      flowSpecs_1.12.0     CytoML_2.10.0        flowWorkspace_4.10.1
[36] scico_1.3.1          CytobankAPI_2.2.0    httr_1.4.5           curl_5.0.0           cytotidyr_0.0.1.100  kableExtra_1.3.4     PeacoQC_1.9.3       
[43] infinityFlow_1.8.0   flowCore_2.10.0     

loaded via a namespace (and not attached):
  [1] scattermore_0.8             SeuratObject_4.1.3          ragg_1.2.5                  knitr_1.42                  irlba_2.3.5.1              
  [6] DelayedArray_0.24.0         RCurl_1.98-1.12             doParallel_1.0.17           generics_0.1.3              terra_1.7-23               
 [11] cowplot_1.1.1               RANN_2.6.1                  future_1.32.0               ggpointdensity_0.1.0        tzdb_0.3.0                 
 [16] spatstat.data_3.0-1         webshot_0.5.4               xml2_1.3.3                  httpuv_1.6.9                SummarizedExperiment_1.28.0
 [21] xfun_0.38                   hms_1.1.3                   jquerylib_0.1.4             evaluate_0.20               promises_1.2.0.1           
 [26] DEoptimR_1.0-12             fansi_1.0.4                 Rgraphviz_2.42.0            DBI_1.1.3                   htmlwidgets_1.6.2          
 [31] spatstat.geom_3.1-0         stats4_4.2.3                matlab_1.0.4                ellipsis_0.3.2              RSpectra_0.16-1            
 [36] ks_1.14.0                   backports_1.4.1             ggpubr_0.6.0                ggnewscale_0.4.8            cytolib_2.10.1             
 [41] deldir_1.0-6                MatrixGenerics_1.10.0       vctrs_0.6.1                 SingleCellExperiment_1.20.1 ROCR_1.0-11                
 [46] abind_1.4-5                 cachem_1.0.7                withr_2.5.0                 ggforce_0.4.1               robustbase_0.95-1          
 [51] progressr_0.13.0            sctransform_0.3.5.9002      mclust_6.0.0                mnormt_2.1.1                goftest_1.2-3              
 [56] svglite_2.1.1               cluster_2.1.4               lazyeval_0.2.2              crayon_1.5.2                spatstat.explore_3.1-0     
 [61] pkgconfig_2.0.3             labeling_0.4.2              tweenr_2.0.2                GenomeInfoDb_1.34.9         nlme_3.1-162               
 [66] rlang_1.1.0                 globals_0.16.2              lifecycle_1.0.3.9000        miniUI_0.1.1.1              rsvd_1.0.5                 
 [71] polyclip_1.10-4             matrixStats_0.63.0          lmtest_0.9-40               graph_1.76.0                Matrix_1.5-4               
 [76] raster_3.6-20               carData_3.0-5               zoo_1.8-11                  base64enc_0.1-3             whisker_0.4.1              
 [81] ggridges_0.5.4              GlobalOptions_0.1.2         png_0.1-8                   viridisLite_0.4.1           rjson_0.2.21               
 [86] bitops_1.0-7                ConsensusClusterPlus_1.62.0 KernSmooth_2.23-20          shape_1.4.6                 parallelly_1.35.0          
 [91] spatstat.random_3.1-4       rstatix_0.7.2               jpeg_0.1-10                 ggsignif_0.6.4              S4Vectors_0.36.2           
 [96] magrittr_2.0.3              plyr_1.8.8                  hexbin_1.28.3               ica_1.0-3                   openCyto_2.10.1            
[101] zlibbioc_1.44.0             hdrcde_3.4                  compiler_4.2.3              clue_0.3-64                 rrcov_1.7-2                
[106] fitdistrplus_1.1-8          cli_3.6.1                   XVector_0.38.0              listenv_0.9.0               patchwork_1.1.2.9000       
[111] pbapply_1.7-0               MASS_7.3-58.3               tidyselect_1.2.0            stringi_1.7.12              RProtoBufLib_2.10.0        
[116] textshaping_0.3.6           highr_0.10                  yaml_2.3.7                  askpass_1.1                 latticeExtra_0.6-30        
[121] ggrepel_0.9.3               sass_0.4.5                  tools_4.2.3                 timechange_0.2.0            future.apply_1.10.0        
[126] parallel_4.2.3              circlize_0.4.15             rstudioapi_0.14             foreach_1.5.2               farver_2.1.1               
[131] Rtsne_0.16                  digest_0.6.31               pracma_2.4.2                shiny_1.7.4                 Rcpp_1.0.10                
[136] car_3.1-2                   broom_1.0.4                 GenomicRanges_1.50.2        later_1.3.0                 fda_6.0.5                  
[141] RcppAnnoy_0.0.20            IDPmisc_1.1.20              ComplexHeatmap_2.14.0       colorspace_2.1-0            rainbow_3.7                
[146] rvest_1.0.3                 XML_3.99-0.14               tensor_1.5                  reticulate_1.28             IRanges_2.32.0             
[151] splines_4.2.3               uwot_0.1.14                 RBGL_1.74.0                 spatstat.utils_3.0-2        sp_1.6-0                   
[156] plotly_4.10.1.9000          systemfonts_1.0.4           xtable_1.8-4                fds_1.8                     jsonlite_1.8.4             
[161] corpcor_1.6.10              zeallot_0.1.0               R6_2.5.1                    pillar_1.9.0                htmltools_0.5.5            
[166] mime_0.12                   glue_1.6.2                  fastmap_1.1.1               BiocParallel_1.32.6         deSolve_1.35               
[171] codetools_0.2-19            pcaPP_2.0-3                 mvtnorm_1.1-3               utf8_1.2.3                  bslib_0.4.2                
[176] spatstat.sparse_3.0-1       leiden_0.4.3                tfruns_1.5.1                openssl_2.0.6               interp_1.1-4               
[181] survival_3.5-5              rmarkdown_2.21              munsell_0.5.0               GetoptLong_1.0.5            GenomeInfoDbData_1.2.9     
[186] iterators_1.0.14            reshape2_1.4.4              gtable_0.3.3                Seurat_4.3.0
denvercal1234GitHub commented 1 year ago

Reinstalled the package