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 4.3.0 RC (2023-04-13 r84266)
#> Platform: aarch64-apple-darwin20 (64-bit)
#> Running under: macOS Monterey 12.6.1
#> 
#> 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_1.1.2             scater_1.28.0              
#>  [3] ggplot2_3.4.2               scuttle_1.10.1             
#>  [5] bluster_1.10.0              BiocNeighbors_1.18.0       
#>  [7] TENxPBMCData_1.17.0         HDF5Array_1.28.1           
#>  [9] rhdf5_2.44.0                DelayedArray_0.26.2        
#> [11] S4Arrays_1.0.1              Matrix_1.5-4               
#> [13] SingleCellExperiment_1.22.0 SummarizedExperiment_1.30.1
#> [15] Biobase_2.60.0              GenomicRanges_1.52.0       
#> [17] GenomeInfoDb_1.36.0         IRanges_2.34.0             
#> [19] S4Vectors_0.38.1            BiocGenerics_0.46.0        
#> [21] MatrixGenerics_1.12.0       matrixStats_0.63.0         
#> [23] concordexR_1.0.0            BiocStyle_2.28.0           
#> 
#> loaded via a namespace (and not attached):
#>   [1] RColorBrewer_1.1-3            jsonlite_1.8.4               
#>   [3] magrittr_2.0.3                ggbeeswarm_0.7.1             
#>   [5] magick_2.7.4                  farver_2.1.1                 
#>   [7] rmarkdown_2.21                zlibbioc_1.46.0              
#>   [9] vctrs_0.6.1                   memoise_2.0.1                
#>  [11] DelayedMatrixStats_1.22.0     RCurl_1.98-1.12              
#>  [13] htmltools_0.5.5               AnnotationHub_3.8.0          
#>  [15] curl_5.0.0                    Rhdf5lib_1.22.0              
#>  [17] sass_0.4.5                    bslib_0.4.2                  
#>  [19] cachem_1.0.7                  igraph_1.4.2                 
#>  [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_1.2.10       shiny_1.7.4                  
#>  [29] digest_0.6.31                 colorspace_2.1-0             
#>  [31] AnnotationDbi_1.62.1          irlba_2.3.5.1                
#>  [33] ExperimentHub_2.8.0           RSQLite_2.3.1                
#>  [35] beachmat_2.16.0               filelock_1.0.2               
#>  [37] labeling_0.4.2                fansi_1.0.4                  
#>  [39] httr_1.4.5                    compiler_4.3.0               
#>  [41] bit64_4.0.5                   withr_2.5.0                  
#>  [43] BiocParallel_1.34.1           viridis_0.6.2                
#>  [45] DBI_1.1.3                     highr_0.10                   
#>  [47] MASS_7.3-58.4                 rappdirs_0.3.3               
#>  [49] tools_4.3.0                   vipor_0.4.5                  
#>  [51] beeswarm_0.4.0                interactiveDisplayBase_1.38.0
#>  [53] httpuv_1.6.9                  glue_1.6.2                   
#>  [55] rhdf5filters_1.12.1           promises_1.2.0.1             
#>  [57] grid_4.3.0                    cluster_2.1.4                
#>  [59] generics_0.1.3                isoband_0.2.7                
#>  [61] gtable_0.3.3                  BiocSingular_1.16.0          
#>  [63] ScaledMatrix_1.8.1            utf8_1.2.3                   
#>  [65] XVector_0.40.0                ggrepel_0.9.3                
#>  [67] BiocVersion_3.17.1            pillar_1.9.0                 
#>  [69] later_1.3.0                   dplyr_1.1.1                  
#>  [71] BiocFileCache_2.8.0           lattice_0.21-8               
#>  [73] FNN_1.1.3.2                   bit_4.0.5                    
#>  [75] tidyselect_1.2.0              Biostrings_2.68.0            
#>  [77] knitr_1.42                    gridExtra_2.3                
#>  [79] bookdown_0.33                 xfun_0.38                    
#>  [81] pheatmap_1.0.12               yaml_2.3.7                   
#>  [83] evaluate_0.20                 codetools_0.2-19             
#>  [85] tibble_3.2.1                  BiocManager_1.30.20          
#>  [87] cli_3.6.1                     uwot_0.1.14                  
#>  [89] xtable_1.8-4                  munsell_0.5.0                
#>  [91] jquerylib_0.1.4               Rcpp_1.0.10                  
#>  [93] dbplyr_2.3.2                  png_0.1-8                    
#>  [95] parallel_4.3.0                ellipsis_0.3.2               
#>  [97] blob_1.2.4                    sparseMatrixStats_1.12.0     
#>  [99] bitops_1.0-7                  viridisLite_0.4.1            
#> [101] scales_1.2.1                  purrr_1.0.1                  
#> [103] crayon_1.5.2                  rlang_1.1.0                  
#> [105] cowplot_1.1.1                 KEGGREST_1.40.0