# Overview of concordexR

Lambda Moses, Kayla Jackson

#### Apr 25, 2023

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
    #>  [17] ellipsis_0.3.2                labeling_0.4.2
    #>  [19] utf8_1.2.3                    promises_1.2.0.1
    #>  [21] rmarkdown_2.21                ggbeeswarm_0.7.1
    #>  [23] purrr_1.0.1                   bit_4.0.5
    #>  [25] xfun_0.39                     zlibbioc_1.46.0
    #>  [27] cachem_1.0.7                  beachmat_2.16.0
    #>  [29] jsonlite_1.8.4                blob_1.2.4
    #>  [31] highr_0.10                    later_1.3.0
    #>  [33] rhdf5filters_1.12.0           Rhdf5lib_1.22.0
    #>  [35] BiocParallel_1.34.0           interactiveDisplayBase_1.38.0
    #>  [37] irlba_2.3.5.1                 parallel_4.3.0
    #>  [39] cluster_2.1.4                 R6_2.5.1
    #>  [41] bslib_0.4.2                   RColorBrewer_1.1-3
    #>  [43] jquerylib_0.1.4               Rcpp_1.0.10
    #>  [45] bookdown_0.33                 knitr_1.42
    #>  [47] FNN_1.1.3.2                   httpuv_1.6.9
    #>  [49] igraph_1.4.2                  tidyselect_1.2.0
    #>  [51] viridis_0.6.2                 yaml_2.3.7
    #>  [53] codetools_0.2-19              curl_5.0.0
    #>  [55] lattice_0.21-8                tibble_3.2.1
    #>  [57] withr_2.5.0                   shiny_1.7.4
    #>  [59] KEGGREST_1.40.0               evaluate_0.20
    #>  [61] isoband_0.2.7                 BiocFileCache_2.8.0
    #>  [63] ExperimentHub_2.8.0           Biostrings_2.68.0
    #>  [65] pillar_1.9.0                  BiocManager_1.30.20
    #>  [67] filelock_1.0.2                generics_0.1.3
    #>  [69] RCurl_1.98-1.12               BiocVersion_3.17.1
    #>  [71] sparseMatrixStats_1.12.0      munsell_0.5.0
    #>  [73] scales_1.2.1                  xtable_1.8-4
    #>  [75] glue_1.6.2                    pheatmap_1.0.12
    #>  [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
    #>  [87] vipor_0.4.5                   rsvd_1.0.5
    #>  [89] cli_3.6.1                     rappdirs_0.3.3
    #>  [91] fansi_1.0.4                   viridisLite_0.4.1
    #>  [93] dplyr_1.1.2                   uwot_0.1.14
    #>  [95] gtable_0.3.3                  sass_0.4.5
    #>  [97] digest_0.6.31                 ggrepel_0.9.3
    #>  [99] farver_2.1.1                  memoise_2.0.1
    #> [101] htmltools_0.5.5               lifecycle_1.0.3
    #> [103] httr_1.4.5                    mime_0.12
    #> [105] MASS_7.3-59                   bit64_4.0.5