The goal of concordexR is to replace UMAP as a clustering diagnostic.

0.1 Installation

This package can be installed from Bioconductor since version 3.17 with

BiocManager::install("concordexR")

0.2 Example of main functionality

This is a basic example which shows you how to solve a common problem:

library(concordexR)
library(BiocNeighbors)
g <- findKNN(iris[, seq_len(4)], k = 10)
#> Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
#> detected tied distances to neighbors, see ?'BiocNeighbors-ties'
res <- calculateConcordex(g$index, labels = iris$Species, k = 10, return.map = TRUE)
plotConcordexSim(res)

heatConcordex(res)

0.3 SessionInfo

sessionInfo()
#> R version 4.3.2 (2023-10-31)
#> Platform: aarch64-apple-darwin20 (64-bit)
#> Running under: macOS Ventura 13.6.1
#> 
#> Matrix products: default
#> BLAS:   /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRblas.0.dylib 
#> LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.11.0
#> 
#> locale:
#> [1] C/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
#> 
#> time zone: America/New_York
#> tzcode source: internal
#> 
#> attached base packages:
#> [1] stats4    stats     graphics  grDevices utils     datasets  methods  
#> [8] base     
#> 
#> other attached packages:
#>  [1] patchwork_1.1.3             scater_1.30.0              
#>  [3] ggplot2_3.4.4               scuttle_1.12.0             
#>  [5] bluster_1.12.0              BiocNeighbors_1.20.0       
#>  [7] TENxPBMCData_1.20.0         HDF5Array_1.30.0           
#>  [9] rhdf5_2.46.0                DelayedArray_0.28.0        
#> [11] SparseArray_1.2.1           S4Arrays_1.2.0             
#> [13] abind_1.4-5                 Matrix_1.6-1.1             
#> [15] SingleCellExperiment_1.24.0 SummarizedExperiment_1.32.0
#> [17] Biobase_2.62.0              GenomicRanges_1.54.1       
#> [19] GenomeInfoDb_1.38.0         IRanges_2.36.0             
#> [21] S4Vectors_0.40.1            BiocGenerics_0.48.1        
#> [23] MatrixGenerics_1.14.0       matrixStats_1.0.0          
#> [25] concordexR_1.2.0            BiocStyle_2.30.0           
#> 
#> loaded via a namespace (and not attached):
#>   [1] RColorBrewer_1.1-3            jsonlite_1.8.7               
#>   [3] magrittr_2.0.3                ggbeeswarm_0.7.2             
#>   [5] magick_2.8.1                  farver_2.1.1                 
#>   [7] rmarkdown_2.25                zlibbioc_1.48.0              
#>   [9] vctrs_0.6.4                   memoise_2.0.1                
#>  [11] DelayedMatrixStats_1.24.0     RCurl_1.98-1.13              
#>  [13] htmltools_0.5.7               AnnotationHub_3.10.0         
#>  [15] curl_5.1.0                    Rhdf5lib_1.24.0              
#>  [17] sass_0.4.7                    bslib_0.5.1                  
#>  [19] cachem_1.0.8                  igraph_1.5.1                 
#>  [21] mime_0.12                     lifecycle_1.0.3              
#>  [23] pkgconfig_2.0.3               rsvd_1.0.5                   
#>  [25] R6_2.5.1                      fastmap_1.1.1                
#>  [27] GenomeInfoDbData_1.2.11       shiny_1.7.5.1                
#>  [29] digest_0.6.33                 colorspace_2.1-0             
#>  [31] AnnotationDbi_1.64.1          irlba_2.3.5.1                
#>  [33] ExperimentHub_2.10.0          RSQLite_2.3.2                
#>  [35] beachmat_2.18.0               filelock_1.0.2               
#>  [37] labeling_0.4.3                fansi_1.0.5                  
#>  [39] httr_1.4.7                    compiler_4.3.2               
#>  [41] bit64_4.0.5                   withr_2.5.2                  
#>  [43] BiocParallel_1.36.0           viridis_0.6.4                
#>  [45] DBI_1.1.3                     highr_0.10                   
#>  [47] MASS_7.3-60                   rappdirs_0.3.3               
#>  [49] tools_4.3.2                   vipor_0.4.5                  
#>  [51] beeswarm_0.4.0                interactiveDisplayBase_1.40.0
#>  [53] httpuv_1.6.12                 glue_1.6.2                   
#>  [55] rhdf5filters_1.14.1           promises_1.2.1               
#>  [57] grid_4.3.2                    cluster_2.1.4                
#>  [59] generics_0.1.3                isoband_0.2.7                
#>  [61] gtable_0.3.4                  BiocSingular_1.18.0          
#>  [63] ScaledMatrix_1.10.0           utf8_1.2.4                   
#>  [65] XVector_0.42.0                ggrepel_0.9.4                
#>  [67] BiocVersion_3.18.0            pillar_1.9.0                 
#>  [69] later_1.3.1                   dplyr_1.1.3                  
#>  [71] BiocFileCache_2.10.1          lattice_0.22-5               
#>  [73] FNN_1.1.3.2                   bit_4.0.5                    
#>  [75] tidyselect_1.2.0              Biostrings_2.70.1            
#>  [77] knitr_1.45                    gridExtra_2.3                
#>  [79] bookdown_0.36                 xfun_0.41                    
#>  [81] pheatmap_1.0.12               yaml_2.3.7                   
#>  [83] evaluate_0.23                 codetools_0.2-19             
#>  [85] tibble_3.2.1                  BiocManager_1.30.22          
#>  [87] cli_3.6.1                     uwot_0.1.16                  
#>  [89] xtable_1.8-4                  munsell_0.5.0                
#>  [91] jquerylib_0.1.4               Rcpp_1.0.11                  
#>  [93] dbplyr_2.4.0                  png_0.1-8                    
#>  [95] parallel_4.3.2                ellipsis_0.3.2               
#>  [97] blob_1.2.4                    sparseMatrixStats_1.14.0     
#>  [99] bitops_1.0-7                  viridisLite_0.4.2            
#> [101] scales_1.2.1                  purrr_1.0.2                  
#> [103] crayon_1.5.2                  rlang_1.1.1                  
#> [105] cowplot_1.1.1                 KEGGREST_1.42.0