CoveragePlot error

[jmzhang1911]

Hi Developer,

I am following the https://stuartlab.org/signac/articles/pbmc_multiomic guide to construct a Seurat object that contains both RNA and peaks.

When I use the CoveragePlot function, I encounter the following error!

However, when I create a Seurat object that contains only the peaks, the CoveragePlot function works without any issues.

Please forgive me if my usage has caused you to waste your valuable time!
Best regards,
Jimmy

sessionInfo()
R version 4.2.3 (2023-03-15)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /share/zhangjm/software/miniconda3/envs/scverse2/lib/libopenblasp-r0.3.25.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
 [1] GenomicRanges_1.50.2 GenomeInfoDb_1.34.9  IRanges_2.32.0      
 [4] S4Vectors_0.36.2     BiocGenerics_0.44.0  lubridate_1.9.3     
 [7] forcats_1.0.0        stringr_1.5.1        dplyr_1.1.4         
[10] purrr_1.0.2          readr_2.1.5          tidyr_1.3.1         
[13] tibble_3.2.1         ggplot2_3.4.2        tidyverse_2.0.0     
[16] Signac_1.14.0        Seurat_5.0.3         SeuratObject_5.0.2  
[19] sp_2.1-2            

loaded via a namespace (and not attached):
  [1] uuid_1.1-1             spam_2.10-0            fastmatch_1.1-4       
  [4] plyr_1.8.9             igraph_2.0.2           repr_1.1.6            
  [7] lazyeval_0.2.2         splines_4.2.3          RcppHNSW_0.5.0        
 [10] BiocParallel_1.32.6    listenv_0.9.0          scattermore_1.2       
 [13] digest_0.6.35          htmltools_0.5.8.1      fansi_1.0.6           
 [16] magrittr_2.0.3         tensor_1.5             cluster_2.1.6         
 [19] ROCR_1.0-11            tzdb_0.4.0             globals_0.16.2        
 [22] Biostrings_2.66.0      matrixStats_1.1.0      timechange_0.3.0      
 [25] spatstat.sparse_3.0-3  colorspace_2.1-0       ggrepel_0.9.4         
 [28] crayon_1.5.2           RCurl_1.98-1.14        jsonlite_1.8.8        
 [31] progressr_0.14.0       spatstat.data_3.0-3    survival_3.5-7        
 [34] zoo_1.8-12             glue_1.7.0             polyclip_1.10-6       
 [37] gtable_0.3.4           zlibbioc_1.44.0        XVector_0.38.0        
 [40] leiden_0.4.3.1         future.apply_1.11.1    abind_1.4-5           
 [43] scales_1.3.0           spatstat.random_3.2-2  miniUI_0.1.1.1        
 [46] Rcpp_1.0.12            viridisLite_0.4.2      xtable_1.8-4          
 [49] reticulate_1.34.0      bit_4.0.5              dotCall64_1.1-1       
 [52] htmlwidgets_1.6.4      httr_1.4.7             RColorBrewer_1.1-3    
 [55] ellipsis_0.3.2         ica_1.0-3              farver_2.1.1          
 [58] pkgconfig_2.0.3        uwot_0.1.16            deldir_2.0-2          
 [61] utf8_1.2.4             labeling_0.4.3         tidyselect_1.2.1      
 [64] rlang_1.1.3            reshape2_1.4.4         later_1.3.2           
 [67] munsell_0.5.0          tools_4.2.3            cli_3.6.2             
 [70] generics_0.1.3         ggridges_0.5.4         evaluate_0.23         
 [73] fastmap_1.1.1          goftest_1.2-3          bit64_4.0.5           
 [76] fitdistrplus_1.1-11    RANN_2.6.1             pbapply_1.7-2         
 [79] future_1.33.1          nlme_3.1-164           mime_0.12             
 [82] RcppRoll_0.3.1         hdf5r_1.3.5            compiler_4.2.3        
 [85] plotly_4.10.3          png_0.1-8              spatstat.utils_3.1-0  
 [88] stringi_1.8.3          RSpectra_0.16-1        lattice_0.22-5        
 [91] IRdisplay_1.1          Matrix_1.6-4           vctrs_0.6.5           
 [94] pillar_1.9.0           lifecycle_1.0.4        spatstat.geom_3.2-7   
 [97] lmtest_0.9-40          RcppAnnoy_0.0.21       data.table_1.15.4     
[100] cowplot_1.1.2          bitops_1.0-7           irlba_2.3.5.1         
[103] httpuv_1.6.15          patchwork_1.1.3        R6_2.5.1              
[106] promises_1.3.0         KernSmooth_2.23-22     gridExtra_2.3         
[109] parallelly_1.36.0      codetools_0.2-19       fastDummies_1.7.3     
[112] MASS_7.3-60            withr_3.0.0            sctransform_0.4.1     
[115] Rsamtools_2.14.0       GenomeInfoDbData_1.2.9 parallel_4.2.3        
[118] hms_1.1.3              grid_4.2.3             IRkernel_1.3.2        
[121] Rtsne_0.16             pbdZMQ_0.3-10          spatstat.explore_3.2-5
[124] shiny_1.8.0            base64enc_0.1-3       

[timoast]

Not sure what the problem is here, could you show the full code you're using?