<!-- README.md is generated from README.Rmd. Please edit that file -->
# concordexR
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[](https://codecov.io/gh/pachterlab/concordexR)
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The goal of concordexR is to replace UMAP as a clustering diagnostic.
## Installation
You can install the development version of concordexR from
[GitHub](https://github.com/) with:
``` r
# install.packages("devtools")
devtools::install_github("pachterlab/concordexR")
```
## Example
This is a basic example using concordex:
``` r
library(concordexR)
library(BiocNeighbors)
```
``` r
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)
```
``` r
plotConcordexSim(res)
```
<img src="man/figures/README-unnamed-chunk-3-1.png" width="70%" />
``` r
heatConcordex(res)
```
<img src="man/figures/README-unnamed-chunk-4-1.png" width="70%" />
