README.Rmd

---
output: github_document
---

<!-- README.md is generated from README.Rmd. Please edit that file -->

```{r, include = FALSE}
knitr::opts_chunk$set(
    collapse = TRUE,
    comment = "#>",
    fig.path = "man/figures/README-",
    out.width = "70%"
)
```

# concordexR

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

## Installation

This repository is not maintained. It has been moved to [https://github.com/pachterlab/concordexR](https://github.com/pachterlab/concordexR).

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 example}
library(concordexR)
library(BiocNeighbors)
```

```{r}
g <- findKNN(iris[, seq_len(4)], k = 10)
res <- calculateConcordex(g$index, labels = iris$Species, k = 10, return.map = TRUE)
```

```{r}
plotConcordexSim(res)
```

```{r}
heatConcordex(res)
```