loops and maxDistance arguments compatibility issues

Hi Jacques,

Thanks for creating this great package. There seems to be an issue visualizing loops on a matrix when trying to combine the loops and maxDistance arguments in the plotMatrix function. For simplification purposes I'm attaching an example of the same two plots with or without the maxDistance argument + the session.info, but if you need more details just let me know.

Thanks !

p1<-plotMatrix(
  hic_4DN_DE_4k, loops = loops, 
  limits = c(-1, 1),
  caption = FALSE)

p2<-plotMatrix(
  hic_4DN_DE_4k, loops = loops, 
  limits = c(-1, 1),
  maxDistance=2000000,
  caption = FALSE)

wrap_plots(p1, p2, ncol = 1)

> sessionInfo()
R version 4.4.1 (2024-06-14)
Platform: aarch64-apple-darwin20
Running under: macOS Sonoma 14.5

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

other attached packages:
[1] patchwork_1.2.0     here_1.0.1          HiContacts_1.6.0   
[4] HiCExperiment_1.4.0

loaded via a namespace (and not attached):
 [1] tidyselect_1.2.1            farver_2.1.2               
 [3] dplyr_1.1.4                 vipor_0.4.7                
 [5] Biostrings_2.72.1           bitops_1.0-7               
 [7] RCurl_1.98-1.16             GenomicAlignments_1.40.0   
 [9] plyinteractions_1.2.0       XML_3.99-0.17              
[11] lifecycle_1.0.4             Cairo_1.6-2                
[13] plyranges_1.24.0            magrittr_2.0.3             
[15] compiler_4.4.1              rlang_1.1.4                
[17] tools_4.4.1                 yaml_2.3.9                 
[19] utf8_1.2.4                  rtracklayer_1.64.0         
[21] labeling_0.4.3              S4Arrays_1.4.1             
[23] bit_4.0.5                   curl_5.2.1                 
[25] DelayedArray_0.30.1         abind_1.4-5                
[27] BiocParallel_1.38.0         withr_3.0.0                
[29] purrr_1.0.2                 BiocGenerics_0.50.0        
[31] grid_4.4.1                  stats4_4.4.1               
[33] fansi_1.0.6                 colorspace_2.1-0           
[35] Rhdf5lib_1.26.0             ggplot2_3.5.1              
[37] scales_1.3.0                SummarizedExperiment_1.34.0
[39] cli_3.6.3                   crayon_1.5.3               
[41] generics_0.1.3              rstudioapi_0.16.0          
[43] RSpectra_0.16-2             rjson_0.2.21               
[45] httr_1.4.7                  tzdb_0.4.0                 
[47] ggbeeswarm_0.7.2            rhdf5_2.48.0               
[49] stringr_1.5.1               zlibbioc_1.50.0            
[51] parallel_4.4.1              ggrastr_1.0.2              
[53] XVector_0.44.0              restfulr_0.0.15            
[55] matrixStats_1.3.0           vctrs_0.6.5                
[57] Matrix_1.7-0                jsonlite_1.8.8             
[59] IRanges_2.38.1              hms_1.1.3                  
[61] S4Vectors_0.42.1            bit64_4.0.5                
[63] beeswarm_0.4.0              strawr_0.0.92              
[65] tidyr_1.3.1                 glue_1.7.0                 
[67] codetools_0.2-20            cowplot_1.1.3              
[69] stringi_1.8.4               gtable_0.3.5               
[71] GenomeInfoDb_1.40.1         BiocIO_1.14.0              
[73] GenomicRanges_1.56.1        UCSC.utils_1.0.0           
[75] munsell_0.5.1               tibble_3.2.1               
[77] pillar_1.9.0                rhdf5filters_1.16.0        
[79] GenomeInfoDbData_1.2.12     R6_2.5.1                   
[81] rprojroot_2.0.4             vroom_1.6.5                
[83] lattice_0.22-6              Biobase_2.64.0             
[85] readr_2.1.5                 Rsamtools_2.20.0           
[87] Rcpp_1.0.13                 InteractionSet_1.32.0      
[89] SparseArray_1.4.8           fs_1.6.4                   
[91] MatrixGenerics_1.16.0       pkgconfig_2.0.3

js2264 / HiContacts

loops and maxDistance arguments compatibility issues #9