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

1 Installation

This package can be installed from Bioconductor since version 3.17 with

BiocManager::install("concordexR")

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)

3 SessionInfo

sessionInfo()
#> R version 4.4.0 alpha (2024-03-27 r86216)
#> Platform: aarch64-apple-darwin20
#> Running under: macOS Ventura 13.6.5
#> 
#> Matrix products: default
#> BLAS:   /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRblas.0.dylib 
#> LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.0
#> 
#> 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: America/New_York
#> tzcode source: internal
#> 
#> attached base packages:
#> [1] stats4    stats     graphics  grDevices utils     datasets  methods  
#> [8] base     
#> 
#> other attached packages:
#>  [1] patchwork_1.2.0             scater_1.32.0              
#>  [3] ggplot2_3.5.0               scuttle_1.14.0             
#>  [5] bluster_1.14.0              BiocNeighbors_1.22.0       
#>  [7] TENxPBMCData_1.21.0         HDF5Array_1.32.0           
#>  [9] rhdf5_2.48.0                DelayedArray_0.30.0        
#> [11] SparseArray_1.4.0           S4Arrays_1.4.0             
#> [13] abind_1.4-5                 Matrix_1.7-0               
#> [15] SingleCellExperiment_1.26.0 SummarizedExperiment_1.34.0
#> [17] Biobase_2.64.0              GenomicRanges_1.56.0       
#> [19] GenomeInfoDb_1.40.0         IRanges_2.38.0             
#> [21] S4Vectors_0.42.0            BiocGenerics_0.50.0        
#> [23] MatrixGenerics_1.16.0       matrixStats_1.2.0          
#> [25] concordexR_1.4.0            BiocStyle_2.32.0           
#> 
#> loaded via a namespace (and not attached):
#>  [1] DBI_1.2.2                 gridExtra_2.3            
#>  [3] rlang_1.1.3               magrittr_2.0.3           
#>  [5] compiler_4.4.0            RSQLite_2.3.5            
#>  [7] DelayedMatrixStats_1.26.0 png_0.1-8                
#>  [9] vctrs_0.6.5               pkgconfig_2.0.3          
#> [11] crayon_1.5.2              fastmap_1.1.1            
#> [13] magick_2.8.3              dbplyr_2.5.0             
#> [15] XVector_0.44.0            labeling_0.4.3           
#> [17] utf8_1.2.4                rmarkdown_2.26           
#> [19] ggbeeswarm_0.7.2          UCSC.utils_1.0.0         
#> [21] purrr_1.0.2               bit_4.0.5                
#> [23] xfun_0.43                 zlibbioc_1.50.0          
#> [25] cachem_1.0.8              beachmat_2.20.0          
#> [27] jsonlite_1.8.8            blob_1.2.4               
#> [29] highr_0.10                rhdf5filters_1.16.0      
#> [31] Rhdf5lib_1.26.0           BiocParallel_1.38.0      
#> [33] irlba_2.3.5.1             parallel_4.4.0           
#> [35] cluster_2.1.6             R6_2.5.1                 
#> [37] bslib_0.6.2               RColorBrewer_1.1-3       
#> [39] jquerylib_0.1.4           Rcpp_1.0.12              
#> [41] bookdown_0.38             knitr_1.45               
#> [43] FNN_1.1.4                 igraph_2.0.3             
#> [45] tidyselect_1.2.1          viridis_0.6.5            
#> [47] yaml_2.3.8                codetools_0.2-19         
#> [49] curl_5.2.1                lattice_0.22-6           
#> [51] tibble_3.2.1              withr_3.0.0              
#> [53] KEGGREST_1.44.0           evaluate_0.23            
#> [55] isoband_0.2.7             BiocFileCache_2.12.0     
#> [57] ExperimentHub_2.12.0      Biostrings_2.72.0        
#> [59] pillar_1.9.0              BiocManager_1.30.22      
#> [61] filelock_1.0.3            generics_0.1.3           
#> [63] BiocVersion_3.19.1        sparseMatrixStats_1.16.0 
#> [65] munsell_0.5.0             scales_1.3.0             
#> [67] glue_1.7.0                pheatmap_1.0.12          
#> [69] tools_4.4.0               AnnotationHub_3.12.0     
#> [71] ScaledMatrix_1.12.0       cowplot_1.1.3            
#> [73] grid_4.4.0                AnnotationDbi_1.66.0     
#> [75] colorspace_2.1-0          GenomeInfoDbData_1.2.12  
#> [77] beeswarm_0.4.0            BiocSingular_1.20.0      
#> [79] vipor_0.4.7               rsvd_1.0.5               
#> [81] cli_3.6.2                 rappdirs_0.3.3           
#> [83] fansi_1.0.6               viridisLite_0.4.2        
#> [85] dplyr_1.1.4               uwot_0.1.16              
#> [87] gtable_0.3.4              sass_0.4.9               
#> [89] digest_0.6.35             ggrepel_0.9.5            
#> [91] farver_2.1.1              memoise_2.0.1            
#> [93] htmltools_0.5.8           lifecycle_1.0.4          
#> [95] httr_1.4.7                mime_0.12                
#> [97] MASS_7.3-60.2             bit64_4.0.5