# Overview of concordexR

Lambda Moses, Kayla Jackson

#### May 01, 2024

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 ucrt)
    #> Platform: x86_64-w64-mingw32/x64
    #> Running under: Windows Server 2022 x64 (build 20348)
    #>
    #> Matrix products: default
    #>
    #>
    #> locale:
    #> [1] LC_COLLATE=C
    #> [2] LC_CTYPE=English_United States.utf8
    #> [3] LC_MONETARY=English_United States.utf8
    #> [4] LC_NUMERIC=C
    #> [5] LC_TIME=English_United States.utf8
    #>
    #> 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_3.5.1               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