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 4.3.1 (2023-06-16)
#> Platform: x86_64-pc-linux-gnu (64-bit)
#> Running under: Ubuntu 22.04.3 LTS
#> 
#> Matrix products: default
#> BLAS:   /home/biocbuild/bbs-3.18-bioc/R/lib/libRblas.so 
#> LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0
#> 
#> locale:
#>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
#>  [3] LC_TIME=en_GB              LC_COLLATE=C              
#>  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
#>  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
#>  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
#> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
#> 
#> time zone: America/New_York
#> tzcode source: system (glibc)
#> 
#> 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_1.19.0         HDF5Array_1.30.0           
#>  [9] rhdf5_2.46.0                DelayedArray_0.28.0        
#> [11] SparseArray_1.2.0           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_1.54.0       
#> [19] GenomeInfoDb_1.38.0         IRanges_2.36.0             
#> [21] S4Vectors_0.40.0            BiocGenerics_0.48.0        
#> [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_1.98-1.12              
#>  [13] htmltools_0.5.6.1             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_1.64.0          irlba_2.3.5.1                
#>  [33] ExperimentHub_2.10.0          RSQLite_2.3.1                
#>  [35] beachmat_2.18.0               filelock_1.0.2               
#>  [37] labeling_0.4.3                fansi_1.0.5                  
#>  [39] httr_1.4.7                    compiler_4.3.1               
#>  [41] bit64_4.0.5                   withr_2.5.1                  
#>  [43] BiocParallel_1.36.0           viridis_0.6.4                
#>  [45] DBI_1.1.3                     MASS_7.3-60                  
#>  [47] rappdirs_0.3.3                tools_4.3.1                  
#>  [49] vipor_0.4.5                   beeswarm_0.4.0               
#>  [51] interactiveDisplayBase_1.40.0 httpuv_1.6.12                
#>  [53] glue_1.6.2                    rhdf5filters_1.14.0          
#>  [55] promises_1.2.1                grid_4.3.1                   
#>  [57] cluster_2.1.4                 generics_0.1.3               
#>  [59] isoband_0.2.7                 gtable_0.3.4                 
#>  [61] BiocSingular_1.18.0           ScaledMatrix_1.10.0          
#>  [63] utf8_1.2.4                    XVector_0.42.0               
#>  [65] ggrepel_0.9.4                 BiocVersion_3.18.0           
#>  [67] pillar_1.9.0                  later_1.3.1                  
#>  [69] dplyr_1.1.3                   BiocFileCache_2.10.0         
#>  [71] lattice_0.22-5                FNN_1.1.3.2                  
#>  [73] bit_4.0.5                     tidyselect_1.2.0             
#>  [75] Biostrings_2.70.0             knitr_1.44                   
#>  [77] gridExtra_2.3                 bookdown_0.36                
#>  [79] xfun_0.40                     pheatmap_1.0.12              
#>  [81] yaml_2.3.7                    evaluate_0.22                
#>  [83] codetools_0.2-19              tibble_3.2.1                 
#>  [85] BiocManager_1.30.22           cli_3.6.1                    
#>  [87] uwot_0.1.16                   xtable_1.8-4                 
#>  [89] munsell_0.5.0                 jquerylib_0.1.4              
#>  [91] Rcpp_1.0.11                   dbplyr_2.3.4                 
#>  [93] png_0.1-8                     parallel_4.3.1               
#>  [95] ellipsis_0.3.2                blob_1.2.4                   
#>  [97] sparseMatrixStats_1.14.0      bitops_1.0-7                 
#>  [99] viridisLite_0.4.2             scales_1.2.1                 
#> [101] purrr_1.0.2                   crayon_1.5.2                 
#> [103] rlang_1.1.1                   cowplot_1.1.1                
#> [105] KEGGREST_1.42.0