---
title: "Cluster Analysis"
author: "Sebastian Hönel"
date: "`r Sys.Date()`"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{Cluster Analysis}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

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

> In this vignette, we are evaluating neighborhood-search, network-centralities and vicinities using Bayesian estimators as implemented in *mmb*.


# Vicinity Example
Using some gradient-coloring:

```{r}
library(mmb)
library(Rtsne)
library(ggplot2)
library(ggpubr)

set.seed(1)
chooseSample <- 1

df <- iris[sample(rownames(iris)), ]
#df <- iris[,]
tsne <- Rtsne::Rtsne(df[, 1:4], check_duplicates = FALSE)
# Attach:
df$X <- tsne$Y[, 1]
df$Y <- tsne$Y[, 2]

# Let's pick one sample to calculate the vicinity for:
s <- df[chooseSample, 1:4]
vics <- mmb::vicinitiesForSample(doEcdf = FALSE, shiftAmount = 1,
  df = df[, 1:4], sampleFromDf = s, selectedFeatureNames = colnames(s),
  retainMinValues = 5)

# Attach to df:
df$vics <- vics$vicinity
# TEMP TEMP TEMP: Discretize vics
mmbd <- mmb::discretizeVariableToRanges(df$vics, numRanges = length(levels(df$Species)))
df$vicsD <- sapply(df$vics, function(v) {
  for (i in 1:length(mmbd)) {
    r <- mmbd[[i]]
    if (v >= r[1] && v < r[2]) return(paste("R", i, sep = "_"))
  }
})

# Also, create a binary classification:
df$vicsB <- sapply(df$vics, function(v) {
  return(if (v > 0.1) "P" else "N")
})

# Additionally, compute the Euclidean-distance:
df$vicsE <- as.vector(philentropy::distance(df[, 1:4])[1,])
df$vicsE <- max(df$vicsE) - df$vicsE

pointCommon <- geom_point(shape=1, size=3, color="#000000", data=df[chooseSample,], mapping=aes(x=df[chooseSample,]$X, y=df[chooseSample,]$Y))


g1 <- ggplot(df, aes(x=X, y=Y, color=Species)) +
  geom_point() +
  pointCommon +
  stat_ellipse()

g2 <- ggplot(df, aes(x=X, y=Y)) +
  geom_point(aes(color=vics)) +
  #stat_ellipse() +
  scale_color_gradient(low="blue", high="red")

# TEMP TEMP TEMP
g3 <- ggplot(df, aes(x=X, y=Y, color=vicsD)) +
  geom_point() #+
  #stat_ellipse()

g4 <- ggplot(df, aes(x=X, y=Y, color=vicsB)) +
  geom_point() +
  stat_ellipse()

g5 <- ggplot(df, aes(x=X, y=Y)) +
  geom_point(aes(color=vicsE)) +
  #stat_ellipse() +
  scale_color_gradient(low="blue", high="red")

ggarrange(g1, g2, g3, g4, g5)
```