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 4.4.0 beta (2024-04-15 r86425)
#> Platform: x86_64-pc-linux-gnu
#> Running under: Ubuntu 22.04.4 LTS
#> 
#> Matrix products: default
#> BLAS:   /home/biocbuild/bbs-3.19-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_US.UTF-8        LC_COLLATE=en_US.UTF-8    
#>  [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_1.2.0             scater_1.32.0              
#>  [3] ggplot2_3.5.1               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_1.3.0          
#> [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_2.3.6            
#>  [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] tinytex_0.50              purrr_1.0.2              
#> [23] bit_4.0.5                 xfun_0.43                
#> [25] zlibbioc_1.50.0           cachem_1.0.8             
#> [27] beachmat_2.20.0           jsonlite_1.8.8           
#> [29] blob_1.2.4                highr_0.10               
#> [31] rhdf5filters_1.16.0       Rhdf5lib_1.26.0          
#> [33] BiocParallel_1.38.0       irlba_2.3.5.1            
#> [35] parallel_4.4.0            cluster_2.1.6            
#> [37] R6_2.5.1                  bslib_0.7.0              
#> [39] RColorBrewer_1.1-3        jquerylib_0.1.4          
#> [41] Rcpp_1.0.12               bookdown_0.39            
#> [43] knitr_1.46                FNN_1.1.4                
#> [45] igraph_2.0.3              tidyselect_1.2.1         
#> [47] viridis_0.6.5             yaml_2.3.8               
#> [49] codetools_0.2-20          curl_5.2.1               
#> [51] lattice_0.22-6            tibble_3.2.1             
#> [53] withr_3.0.0               KEGGREST_1.44.0          
#> [55] evaluate_0.23             isoband_0.2.7            
#> [57] BiocFileCache_2.12.0      ExperimentHub_2.12.0     
#> [59] Biostrings_2.72.0         pillar_1.9.0             
#> [61] BiocManager_1.30.22       filelock_1.0.3           
#> [63] generics_0.1.3            BiocVersion_3.19.1       
#> [65] sparseMatrixStats_1.16.0  munsell_0.5.1            
#> [67] scales_1.3.0              glue_1.7.0               
#> [69] pheatmap_1.0.12           tools_4.4.0              
#> [71] AnnotationHub_3.12.0      ScaledMatrix_1.12.0      
#> [73] cowplot_1.1.3             grid_4.4.0               
#> [75] AnnotationDbi_1.66.0      colorspace_2.1-0         
#> [77] GenomeInfoDbData_1.2.12   beeswarm_0.4.0           
#> [79] BiocSingular_1.20.0       vipor_0.4.7              
#> [81] rsvd_1.0.5                cli_3.6.2                
#> [83] rappdirs_0.3.3            fansi_1.0.6              
#> [85] viridisLite_0.4.2         dplyr_1.1.4              
#> [87] uwot_0.2.2                gtable_0.3.5             
#> [89] sass_0.4.9                digest_0.6.35            
#> [91] ggrepel_0.9.5             farver_2.1.1             
#> [93] memoise_2.0.1             htmltools_0.5.8.1        
#> [95] lifecycle_1.0.4           httr_1.4.7               
#> [97] mime_0.12                 MASS_7.3-60.2            
#> [99] bit64_4.0.5