clonalCompare does not permit chain="TRB" but rather chain="TRG" and TRA only.

[denvercal1234GitHub]

Hi, Nick,

I was wondering why clonalCompare only can plot TRA and TRG but not TRB for TCRab data?

Also, group.by plots by sample regard of whatever column name is used for this argument.

Would you mind taking a look?

Thank you again!

###### When doing TRB, error
###### When doing TRG, it worked although there is no TRG in my data
Error in str_split(dat[, cloneCall], "_", simplify = TRUE)[, x] : 
  subscript out of bounds

[ncborcherding]

Hey Quang -

What version of scRepertoire are you using?

Can you make a reproducible example with the built-in data?

Thanks,
Nick

[denvercal1234GitHub]

Will make one soon.

It is 2.0.0

Thanks Nick.

> sessionInfo()
R version 4.3.1 (2023-06-16)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Sonoma 14.2.1

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.11.0

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

time zone: Europe/London
tzcode source: internal

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

other attached packages:
[1] cowplot_1.1.2      scRepertoire_2.0.0 tidyr_1.3.0        viridis_0.6.4      viridisLite_0.4.2  ggplot2_3.4.4      gridExtra_2.3     

loaded via a namespace (and not attached):
  [1] hash_2.2.6.3                    igraph_1.6.0                    graph_1.78.0                    ica_1.0-3                      
  [5] plotly_4.10.4                   rematch2_2.1.2                  SingleR_2.2.0                   scater_1.28.0                  
  [9] devtools_2.4.5                  zlibbioc_1.48.0                 tidyselect_1.2.0                bit_4.0.5                      
 [13] doParallel_1.0.17               clue_0.3-65                     lattice_0.22-5                  rjson_0.2.21                   
 [17] evmix_2.12                      blob_1.2.4                      stringr_1.5.1                   urlchecker_1.0.1               
 [21] S4Arrays_1.2.0                  parallel_4.3.1                  Biobase_2.62.0                  png_0.1-8                      
 [25] plotrix_3.8-4                   cli_3.6.2                       flowViz_1.64.0                  ProtGenerics_1.32.0            
 [29] IDPmisc_1.1.20                  CATALYST_1.24.0                 goftest_1.2-3                   BiocIO_1.10.0                  
 [33] bluster_1.10.0                  purrr_1.0.2                     BiocNeighbors_1.18.0            stringdist_0.9.12              
 [37] uwot_0.1.16                     dendextend_1.17.1               curl_5.2.0                      mime_0.12                      
 [41] evaluate_0.23                   leiden_0.4.3.1                  ComplexHeatmap_2.18.0           V8_4.4.1                       
 [45] stringi_1.8.3                   backports_1.4.1                 gsl_2.1-8                       XML_3.99-0.16                  
 [49] lubridate_1.9.3                 httpuv_1.6.13                   flexmix_2.3-19                  AnnotationDbi_1.64.1           
 [53] paletteer_1.5.0                 magrittr_2.0.3                  rappdirs_0.3.3                  splines_4.3.1                  
 [57] mclust_6.0.1                    jpeg_0.1-10                     ncdfFlow_2.46.0                 xlsx_0.6.5                     
 [61] ggraph_2.1.0                    dplyr_1.1.4                     PeacoQC_1.11.2                  DT_0.31                        
 [65] sctransform_0.4.1               ggbeeswarm_0.7.2                sessioninfo_1.2.2               HDF5Array_1.30.0               
 [69] Nebulosa_1.10.0                 ggExtra_0.10.1                  DBI_1.2.0                       withr_3.0.0                    
 [73] lmtest_0.9-40                   ggnewscale_0.4.9                clustree_0.5.1                  tidygraph_1.3.0                
 [77] rtracklayer_1.60.1              BiocManager_1.30.22             htmlwidgets_1.6.4               fs_1.6.3                       
 [81] S4Vectors_0.40.2                biomaRt_2.56.1                  SingleCellExperiment_1.24.0     ggrepel_0.9.5                  
 [85] labeling_0.4.3                  tidyHeatmap_1.10.1              SparseArray_1.2.3               cellranger_1.1.0               
 [89] MatrixGenerics_1.14.0           tidyseurat_0.8.0                reticulate_1.34.0               hexbin_1.28.3                  
 [93] zoo_1.8-12                      GGally_2.2.0                    XVector_0.42.0                  knitr_1.45                     
 [97] nnls_1.5                        drc_3.0-1                       BiocGenerics_0.48.1             timechange_0.2.0               
[101] foreach_1.5.2                   fansi_1.0.6                     dittoSeq_1.12.2                 patchwork_1.2.0                
[105] GoFKernel_2.1-1                 rhdf5_2.46.1                    data.table_1.14.10              quantreg_5.97                  
[109] R.oo_1.25.0                     RSpectra_0.16-1                 irlba_2.3.5.1                   ggrastr_1.0.2                  
[113] fastDummies_1.7.3               ellipsis_0.3.2                  SpatialExperiment_1.12.0        lazyeval_0.2.2                 
[117] yaml_2.3.8                      tidySingleCellExperiment_1.11.6 survival_3.5-7                  scattermore_1.2                
[121] usefun_0.5.0                    BiocVersion_3.18.1              crayon_1.5.2                    RcppAnnoy_0.0.21               
[125] RColorBrewer_1.1-3              progressr_0.14.0                tweenr_2.0.2                    later_1.3.2                    
[129] Rgraphviz_2.44.0                base64enc_0.1-3                 miQC_1.10.0                     ggridges_0.5.5                 
[133] codetools_0.2-19                GlobalOptions_0.1.2             profvis_0.3.8                   Seurat_5.0.1                   
[137] KEGGREST_1.42.0                 Rtsne_0.17                      shape_1.4.6                     flowGate_1.0.0                 
[141] limma_3.56.2                    Rsamtools_2.16.0                filelock_1.0.3                  cytometree_2.0.2               
[145] flowWorkspace_4.12.2            pkgconfig_2.0.3                 xml2_1.3.6                      ggpubr_0.6.0                   
[149] GenomicAlignments_1.36.0        GenomicRanges_1.54.1            IRanges_2.36.0                  evd_2.3-6.1                    
[153] iNEXT_3.0.0                     spatstat.sparse_3.0-3           xtable_1.8-4                    interp_1.1-5                   
[157] car_3.1-2                       plyr_1.8.9                      httr_1.4.7                      tools_4.3.1                    
[161] globals_0.16.2                  SeuratObject_5.0.1              pkgbuild_1.4.3                  beeswarm_0.4.0                 
[165] broom_1.0.5                     nlme_3.1-164                    dbplyr_2.4.0                    ExperimentHub_2.10.0           
[169] MatrixModels_0.5-3              digest_0.6.34                   Spectre_1.0.0                   Matrix_1.6-5                   
[173] farver_2.1.1                    AnnotationFilter_1.24.0         reshape2_1.4.4                  ks_1.14.2                      
[177] glue_1.7.0                      cachem_1.0.8                    BiocFileCache_2.10.1            polyclip_1.10-6                
[181] generics_0.1.3                  Biostrings_2.70.1               ggalluvial_0.12.5               stats4_4.3.1                   
[185] FlowSOM_2.8.0                   mvtnorm_1.2-4                   parallelly_1.36.0               ConsensusClusterPlus_1.64.0    
[189] ggtext_0.1.2                    pkgload_1.3.4                   statmod_1.5.0                   flowCore_2.12.2                
[193] RcppHNSW_0.5.0                  ScaledMatrix_1.8.1              carData_3.0-5                   pbapply_1.7-2                  
[197] randomcoloR_1.1.0.1             SummarizedExperiment_1.32.0     spam_2.10-0                     dqrng_0.3.2                    
[201] utf8_1.2.4                      SeuratWrappers_0.3.2            ontoProc_1.22.0                 graphlayouts_1.0.2             
[205] gtools_3.9.5                    readxl_1.4.3                    ggsignif_0.6.4                  scRNAseq_2.14.0                
[209] shiny_1.8.0                     GenomeInfoDbData_1.2.11         cytolib_2.12.1                  RProtoBufLib_2.12.1            
[213] rhdf5filters_1.14.1             R.utils_2.12.3                  RCurl_1.98-1.14                 memoise_2.0.1                  
[217] rmarkdown_2.25                  LaplacesDemon_16.1.6            paintmap_1.0                    pheatmap_1.0.12                
[221] R.methodsS3_1.8.2               scales_1.3.0                    future_1.33.1                   RANN_2.6.1                     
[225] spatstat.data_3.0-4             rstudioapi_0.15.0               janitor_2.2.0                   cluster_2.1.6                  
[229] spatstat.utils_3.0-4            hms_1.1.3                       fitdistrplus_1.1-11             munsell_0.5.0                  
[233] scCustomize_2.0.1               colorspace_2.1-0                ggdendro_0.1.23                 rlang_1.1.3                    
[237] GenomeInfoDb_1.38.5             pastecs_1.3.21                  DelayedMatrixStats_1.22.6       sparseMatrixStats_1.12.2       
[241] truncdist_1.0-2                 dotCall64_1.1-1                 ggforce_0.4.1                   circlize_0.4.15                
[245] scuttle_1.10.3                  xfun_0.41                       HCATonsilData_1.1.0             TH.data_1.1-2                  
[249] modeltools_0.2-23               remotes_2.4.2.1                 iterators_1.0.14                matrixStats_1.2.0              
[253] abind_1.4-5                     tibble_3.2.1                    interactiveDisplayBase_1.40.0   celldex_1.11.1                 
[257] rJava_1.0-10                    Rhdf5lib_1.24.1                 bitops_1.0-7                    promises_1.2.1                 
[261] RSQLite_2.3.4                   openxlsx_4.2.5.2                sandwich_3.1-0                  DelayedArray_0.28.0            
[265] compiler_4.3.1                  PRROC_1.3.1                     colorRamps_2.3.1                forcats_1.0.0                  
[269] prettyunits_1.2.0               writexl_1.4.2                   boot_1.3-28.1                   beachmat_2.16.0                
[273] SparseM_1.81                    formattable_0.2.1               ttservice_0.4.0                 listenv_0.9.0                  
[277] Rcpp_1.0.12                     edgeR_3.42.4                    AnnotationHub_3.10.0            BiocSingular_1.16.0            
[281] tensor_1.5                      usethis_2.2.2                   MASS_7.3-60.0.1                 progress_1.2.3                 
[285] gridtext_0.1.5                  ontologyPlot_1.6                BiocParallel_1.34.2             cubature_2.1.0                 
[289] spatstat.random_3.2-2           R6_2.5.1                        fastmap_1.1.1                   multcomp_1.4-25                
[293] rstatix_0.7.2                   vipor_0.4.7                     ensembldb_2.24.1                ROCR_1.0-11                    
[297] ggstats_0.5.1                   nnet_7.3-19                     rsvd_1.0.5                      gtable_0.3.4                   
[301] KernSmooth_2.23-22              latticeExtra_0.6-30             miniUI_0.1.1.1                  deldir_2.0-2                   
[305] htmltools_0.5.7                 bit64_4.0.5                     ggprism_1.0.4                   spatstat.explore_3.2-5         
[309] lifecycle_1.0.4                 ggcyto_1.28.1                   zip_2.3.0                       ontologyIndex_2.11             
[313] restfulr_0.0.15                 Scillus_0.5.0                   xlsxjars_0.6.1                  vctrs_0.6.5                    
[317] VGAM_1.1-9                      snakecase_0.11.1                spatstat.geom_3.2-7             scran_1.28.2                   
[321] sp_2.1-2                        SeuratData_0.2.2.9001           pracma_2.4.4                    future.apply_1.11.1            
[325] pillar_1.9.0                    magick_2.8.2                    GenomicFeatures_1.52.2          metapod_1.8.0                  
[329] locfit_1.5-9.8                  jsonlite_1.8.8                  GetoptLong_1.0.5    

[ncborcherding]

Hey Quang,

Nice catch - there was a duplicated chain removal - so anything in the second position was causing an error - should be fixed with the above commit.

Nick

[denvercal1234GitHub]

Hi, @ncborcherding,

Unfortunately, the error persisted as below. Would you mind taking a look?

Thanks, Nick.

#### error with TRB 
> clonalCompare(CD8_VDJ_contig_list_combined, 
+                   top.clones = 50, 
+                   samples = NULL, 
+                   cloneCall="aa", 
+                   graph = "alluvial", group.by = "vdj_donor_ID", exportTable=F, chain="TRB") + theme(legend.position="none")

Error in str_split(dat[, cloneCall], "_", simplify = TRUE)[, x] : 
  subscript out of bounds

#### No error
clonalCompare(CD8_VDJ_contig_list_combined, 
                  top.clones = 50, 
                  samples = NULL, 
                  cloneCall="aa", 
                  graph = "alluvial", group.by = "vdj_donor_ID", exportTable=F, chain="TRA") + theme(legend.position="none")

######### Interestingly, my data is TCRab, but it worked for TCRG; yet, it looks exactly the same as TRA.
clonalCompare(CD8_VDJ_contig_list_combined, 
                  top.clones = 50, 
                  samples = NULL, 
                  cloneCall="aa", 
                  graph = "alluvial", group.by = "vdj_donor_ID", exportTable=F, chain="TRG") + theme(legend.position="none")

[ncborcherding]

Hey Quang - this is actually subtly different issue so I have opened #312 issue.

Basically the issue here is when scRepertoire was constructed simultaneous paired chain profiling TCRA/B + IGH/L or + TRG/D was not considered. The chain handler does not filter by the family and will need to be updated.

For not the rudimentary fix is to subset by cell type, but I will be working on pushing an update between some traveling I am doing.

Thanks for the find!
Nick

[denvercal1234GitHub]

Hi, Nick.

I see. But what you meant by subset by cell type? The data is only TCRab T cells. Did you mean to subset by column TRA or TRB?

> colnames(CD8_VDJ_contig_list_combined[[1]])
 [1] "barcode"            "sample"             "ID"                 "TCR1"               "cdr3_aa1"          
 [6] "cdr3_nt1"           "TCR2"               "cdr3_aa2"           "cdr3_nt2"           "CTgene"            
[11] "CTnt"               "CTaa"               "CTstrict"           "vdj_donor_ID"       "vdj_status"