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 r84269)
#> Platform: x86_64-pc-linux-gnu (64-bit)
#> Running under: Ubuntu 22.04.2 LTS
#> 
#> Matrix products: default
#> BLAS:   /home/biocbuild/bbs-3.17-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_1.1.2             scater_1.28.0              
#>  [3] ggplot2_3.4.2               scuttle_1.10.0             
#>  [5] bluster_1.10.0              BiocNeighbors_1.18.0       
#>  [7] TENxPBMCData_1.17.0         HDF5Array_1.28.0           
#>  [9] rhdf5_2.44.0                DelayedArray_0.26.0        
#> [11] Matrix_1.5-4                SingleCellExperiment_1.22.0
#> [13] SummarizedExperiment_1.30.0 Biobase_2.60.0             
#> [15] GenomicRanges_1.52.0        GenomeInfoDb_1.36.0        
#> [17] IRanges_2.34.0              S4Vectors_0.38.0           
#> [19] BiocGenerics_0.46.0         MatrixGenerics_1.12.0      
#> [21] matrixStats_0.63.0          concordexR_1.0.0           
#> [23] BiocStyle_2.28.0           
#> 
#> loaded via a namespace (and not attached):
#>   [1] DBI_1.1.3                     bitops_1.0-7                 
#>   [3] gridExtra_2.3                 rlang_1.1.0                  
#>   [5] magrittr_2.0.3                compiler_4.3.0               
#>   [7] RSQLite_2.3.1                 DelayedMatrixStats_1.22.0    
#>   [9] png_0.1-8                     vctrs_0.6.2                  
#>  [11] pkgconfig_2.0.3               crayon_1.5.2                 
#>  [13] fastmap_1.1.1                 magick_2.7.4                 
#>  [15] dbplyr_2.3.2                  XVector_0.40.0               
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#>  [19] utf8_1.2.3                    promises_1.2.0.1             
#>  [21] rmarkdown_2.21                ggbeeswarm_0.7.1             
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#>  [77] tools_4.3.0                   AnnotationHub_3.8.0          
#>  [79] ScaledMatrix_1.8.0            cowplot_1.1.1                
#>  [81] grid_4.3.0                    AnnotationDbi_1.62.0         
#>  [83] colorspace_2.1-0              GenomeInfoDbData_1.2.10      
#>  [85] beeswarm_0.4.0                BiocSingular_1.16.0          
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#>  [89] cli_3.6.1                     rappdirs_0.3.3               
#>  [91] fansi_1.0.4                   viridisLite_0.4.1            
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