Links not displaying in CoveragePlot

[amdqiao1]

Hi developers,

I was trying to plot gene-peak links with the CoveragePlot() function, but the links part in the figure was blank despite that links are present in the Signac object. I've tried saving the plot in multiple formats like .png and .pdf but that wasn't helpful. The bottom half of the figure is like below:

Links produced by obj <- LinkPeaks(object = obj, peak.assay = "peaks", expression.assay = "RNA", distance = 100000) are present in my Signac object, and the output of obj@assays[["peaks"]]@links are like following:

GRanges object with 23 ranges and 5 metadata columns:
        seqnames              ranges strand |     score        gene
           <Rle>           <IRanges>  <Rle> | <numeric> <character>
  [122]    chr16   68732379-68737225      * | 0.0518216        CDH1
                          peak    zscore      pvalue
                   <character> <numeric>   <numeric>
  [122] chr16-68732038-68732..   3.93494 4.16082e-05
  -------
  seqinfo: 151 sequences from an unspecified genome; no seqlengths

Here is my pipeline and below is the output of sessionInfo():

R version 4.2.0 (2022-04-22)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: Ubuntu 22.04.3 LTS

Matrix products: default
BLAS/LAPACK: /home/amdqiao/software/miniforge3/envs/1_signac-env/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] reticulate_1.34.0                 lubridate_1.9.2                  
 [3] forcats_1.0.0                     stringr_1.5.1                    
 [5] dplyr_1.1.2                       purrr_1.0.1                      
 [7] readr_2.1.4                       tidyr_1.3.0                      
 [9] tibble_3.2.1                      ggplot2_3.4.2                    
[11] tidyverse_2.0.0                   BSgenome.Hsapiens.UCSC.hg38_1.4.5
[13] BSgenome_1.66.3                   rtracklayer_1.58.0               
[15] Biostrings_2.66.0                 XVector_0.38.0                   
[17] EnsDb.Hsapiens.v86_2.99.0         ensembldb_2.22.0                 
[19] AnnotationFilter_1.22.0           GenomicFeatures_1.50.4           
[21] AnnotationDbi_1.60.2              Biobase_2.58.0                   
[23] GenomicRanges_1.50.2              GenomeInfoDb_1.34.9              
[25] IRanges_2.32.0                    S4Vectors_0.36.2                 
[27] BiocGenerics_0.44.0               DoubletFinder_2.0.4              
[29] Matrix_1.6-3                      SeuratData_0.2.2.9001            
[31] SeuratDisk_0.0.0.9021             SeuratObject_5.0.1               
[33] Seurat_4.3.0                      Signac_1.12.0                    

loaded via a namespace (and not attached):
  [1] utf8_1.2.2                  spatstat.explore_3.2-5     
  [3] tidyselect_1.2.0            RSQLite_2.3.3              
  [5] htmlwidgets_1.6.3           grid_4.2.0                 
  [7] BiocParallel_1.32.6         Rtsne_0.16                 
  [9] munsell_0.5.0               codetools_0.2-19           
 [11] ica_1.0-3                   pbdZMQ_0.3-7               
 [13] future_1.33.0               miniUI_0.1.1.1             
 [15] withr_2.5.2                 spatstat.random_3.2-1      
 [17] colorspace_2.1-0            progressr_0.14.0           
 [19] filelock_1.0.2              uuid_1.1-0                 
 [21] ROCR_1.0-11                 tensor_1.5                 
 [23] listenv_0.9.0               MatrixGenerics_1.10.0      
 [25] repr_1.1.4                  GenomeInfoDbData_1.2.9     
 [27] polyclip_1.10-6             bit64_4.0.5                
 [29] parallelly_1.36.0           vctrs_0.6.4                
 [31] generics_0.1.3              timechange_0.3.0           
 [33] BiocFileCache_2.6.1         R6_2.5.1                   
 [35] hdf5r_1.3.8                 bitops_1.0-7               
 [37] spatstat.utils_3.0-4        cachem_1.0.8               
 [39] DelayedArray_0.24.0         promises_1.2.1             
 [41] BiocIO_1.8.0                scales_1.2.1               
 [43] gtable_0.3.4                globals_0.16.2             
 [45] goftest_1.2-3               spam_2.10-0                
 [47] rlang_1.1.2                 RcppRoll_0.3.0             
 [49] splines_4.2.0               lazyeval_0.2.2             
 [51] spatstat.geom_3.2-7         yaml_2.3.7                 
 [53] reshape2_1.4.4              abind_1.4-5                
 [55] httpuv_1.6.12               tools_4.2.0                
 [57] ellipsis_0.3.2              RColorBrewer_1.1-3         
 [59] ggridges_0.5.4              Rcpp_1.0.11                
 [61] plyr_1.8.9                  base64enc_0.1-3            
 [63] progress_1.2.2              zlibbioc_1.44.0            
 [65] RCurl_1.98-1.13             prettyunits_1.2.0          
 [67] deldir_2.0-2                pbapply_1.7-2              
 [69] cowplot_1.1.1               zoo_1.8-12                 
 [71] SummarizedExperiment_1.28.0 ggrepel_0.9.4              
 [73] cluster_2.1.4               magrittr_2.0.3             
 [75] data.table_1.14.8           scattermore_1.2            
 [77] lmtest_0.9-40               RANN_2.6.1                 
 [79] ProtGenerics_1.30.0         fitdistrplus_1.1-11        
 [81] matrixStats_1.1.0           hms_1.1.3                  
 [83] patchwork_1.1.3             mime_0.12                  
 [85] evaluate_0.23               xtable_1.8-4               
 [87] XML_3.99-0.15               gridExtra_2.3              
 [89] compiler_4.2.0              biomaRt_2.54.1             
 [91] KernSmooth_2.23-22          crayon_1.5.1               
 [93] htmltools_0.5.7             tzdb_0.4.0                 
 [95] later_1.3.1                 DBI_1.1.3                  
 [97] dbplyr_2.4.0                MASS_7.3-60                
 [99] rappdirs_0.3.3              cli_3.6.1                  
[101] parallel_4.2.0              dotCall64_1.1-0            
[103] igraph_1.5.1                pkgconfig_2.0.3            
[105] GenomicAlignments_1.34.1    sp_2.1-2                   
[107] IRdisplay_1.1               plotly_4.10.3              
[109] spatstat.sparse_3.0-3       xml2_1.3.5                 
[111] digest_0.6.33               sctransform_0.4.1          
[113] RcppAnnoy_0.0.21            spatstat.data_3.0-3        
[115] leiden_0.4.3.1              fastmatch_1.1-4            
[117] uwot_0.1.16                 restfulr_0.0.15            
[119] curl_5.1.0                  shiny_1.8.0                
[121] Rsamtools_2.14.0            rjson_0.2.21               
[123] lifecycle_1.0.4             nlme_3.1-163               
[125] jsonlite_1.8.8              viridisLite_0.4.2          
[127] fansi_1.0.3                 pillar_1.9.0               
[129] lattice_0.22-5              KEGGREST_1.38.0            
[131] fastmap_1.1.1               httr_1.4.7                 
[133] survival_3.5-7              glue_1.6.2                 
[135] png_0.1-8                   bit_4.0.5                  
[137] stringi_1.8.2               blob_1.2.4                 
[139] memoise_2.0.1               IRkernel_1.3               
[141] irlba_2.3.5.1               future.apply_1.11.0