---
title: "Introduction: From Clustering to Density Plots"
output: rmarkdown::html_vignette
description: >
  Network-based clustering of binary data. Optional adjustment for covariates. 
vignette: >
  %\VignetteIndexEntry{clustNet}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---



```{r setup}
library(clustNet)
```

## Clustering

First, we need to learn the networks. Here, we simulate data from three clusters. This process takes around two minutes on a local PC.

```{r, message=FALSE, warning=FALSE, results='hide'}
library(clustNet)

# Simulate data
k_clust <- 3 # numer of clusters
ss <- c(400, 500, 600) # samples in each cluster
simulation_data <- sampleData(k_clust = k_clust, n_vars = 20, n_samples = ss)
sampled_data <- simulation_data$sampled_data

# Network-based clustering
cluster_results <- get_clusters(sampled_data, k_clust = k_clust)
```


## Visualization of networks

We can visualize the networks as follows. 

```{r}

# Load additional pacakges to visualize the networks
library(ggplot2)
library(ggraph)
library(igraph)
library(ggpubr)

# Visualize networks
plot_clusters(cluster_results)
```

## Visualization of networks

Finally, we can create a density plot of our clustering. 

```{r}
# Load additional pacakges to create a 2d dimensionality reduction
library(car)
library(ks)
library(graphics)
library(stats)

# Plot a 2d dimensionality reduction
density_plot(cluster_results)
```