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Overview of concordexR

Lambda Moses, Kayla Jackson

Jun 26, 2023

Source: vignettes/overview.Rmd
overview.Rmd

The goal of concordexR is to replace UMAP as a clustering diagnostic.

Installation

This package can be installed from Bioconductor since version 3.17 with

BiocManager::install("concordexR")

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)

SessionInfo 

sessionInfo()
#> R version 4.2.3 (2023-03-15)
#> Platform: x86_64-pc-linux-gnu (64-bit)
#> Running under: Ubuntu 22.04.2 LTS
#> 
#> Matrix products: default
#> BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
#> LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so
#> 
#> locale:
#>  [1] LC_CTYPE=C.UTF-8       LC_NUMERIC=C           LC_TIME=C.UTF-8       
#>  [4] LC_COLLATE=C.UTF-8     LC_MONETARY=C.UTF-8    LC_MESSAGES=C.UTF-8   
#>  [7] LC_PAPER=C.UTF-8       LC_NAME=C              LC_ADDRESS=C          
#> [10] LC_TELEPHONE=C         LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C   
#> 
#> attached base packages:
#> [1] stats     graphics  grDevices utils     datasets  methods   base     
#> 
#> other attached packages:
#> [1] BiocNeighbors_1.16.0 concordexR_0.99.3    BiocStyle_2.26.0    
#> 
#> loaded via a namespace (and not attached):
#>  [1] Rcpp_1.0.10           lattice_0.20-45       rprojroot_2.0.3      
#>  [4] digest_0.6.31         utf8_1.2.3            R6_2.5.1             
#>  [7] stats4_4.2.3          evaluate_0.21         highr_0.10           
#> [10] ggplot2_3.4.2         pillar_1.9.0          rlang_1.1.1          
#> [13] jquerylib_0.1.4       S4Vectors_0.36.2      Matrix_1.5-3         
#> [16] rmarkdown_2.22        pkgdown_2.0.7         textshaping_0.3.6    
#> [19] desc_1.4.2            labeling_0.4.2        BiocParallel_1.32.6  
#> [22] stringr_1.5.0         pheatmap_1.0.12       munsell_0.5.0        
#> [25] DelayedArray_0.24.0   compiler_4.2.3        xfun_0.39            
#> [28] pkgconfig_2.0.3       systemfonts_1.0.4     BiocGenerics_0.44.0  
#> [31] htmltools_0.5.5       tidyselect_1.2.0      tibble_3.2.1         
#> [34] bookdown_0.34         IRanges_2.32.0        codetools_0.2-19     
#> [37] matrixStats_1.0.0     viridisLite_0.4.2     fansi_1.0.4          
#> [40] dplyr_1.1.2           withr_2.5.0           grid_4.2.3           
#> [43] jsonlite_1.8.5        gtable_0.3.3          lifecycle_1.0.3      
#> [46] magrittr_2.0.3        scales_1.2.1          cli_3.6.1            
#> [49] stringi_1.7.12        cachem_1.0.8          farver_2.1.1         
#> [52] fs_1.6.2              bslib_0.5.0           ragg_1.2.5           
#> [55] vctrs_0.6.3           generics_0.1.3        RColorBrewer_1.1-3   
#> [58] tools_4.2.3           glue_1.6.2            purrr_1.0.1          
#> [61] MatrixGenerics_1.10.0 parallel_4.2.3        fastmap_1.1.1        
#> [64] yaml_2.3.7            colorspace_2.1-0      BiocManager_1.30.21  
#> [67] memoise_2.0.1         knitr_1.43            sass_0.4.6