---
title: "Overview of concordexR"
author: "Lambda Moses, Kayla Jackson"
date: "`r format(Sys.Date(), '%b %d, %Y')`"
output:
    BiocStyle::html_document:
        toc: true
        number_sections: true
        toc_depth: 3
        toc_float:
            collapsed: true
vignette: >
  %\VignetteIndexEntry{overview}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

```{r, include = FALSE}
knitr::opts_chunk$set(
    collapse = TRUE,
    comment = "#>", fig.align = "center"
)
```

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 

```{r, eval=FALSE}
BiocManager::install("concordexR")
```

## Example of main functionality

This is a basic example which shows you how to solve a common problem:

```{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)
```

## SessionInfo
```{r}
sessionInfo()
```