---
title: "Understanding the getCoords Function Input"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{getCoords}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

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

# Overview
This vignette describes the usage of the `getCoords` parameter in the `pandemonium` app.

This is an input for a named list of functions that can be used to calculate coordinates. The names of the list will be used as options for the coordinates selector in the GUI. 

Coordinates are a way to put each variable on equal footing before distance calculations. A simple coordinate function is normalising each variable by subtracting the mean and dividing by the standard deviation. The package includes a set of coordinate functions, but other forms are also possible and can be defined as explained below.

# Provided coordinate functions

### `normcoords`

This uses `scale` to center and scale the data.

### `pullCoords()`

Chi-Squared Loss Function Coordinates

### `pullCoordsNoCov()`

Generic Loss Function Coordinates

### `rawCoords()`

Returns the data frame passed to it. This should only be used when the data is already provided as coordinates or coordinate calculations are otherwise impossible.

## `userCoords()`

Used for externally calculated coordinates, to cut down computation time or where a coordinate function cannot otherwise be written.
This is a closure of a coordinate function that returns the user defined coordinate matrix passed to the closure when called in the pandemonium call with `pandemonium(df, getCoords=list(user=userCoords(coordMatrix)))`. This cannot be used when variables are removed from a space through the GUI.

Externally calculated coordinates can be used through userCoords or as input data with rawCoords used as the coordinate function. The use of userCoords over rawCoords is in the treatment of input data. As pandemonium displays the input data in many plots the use of coordinates as input data will result in these plots being less meaningful for interpretation. Use userCoords where coordinates are necessary to calculate distances but interpretation from plots of clustering space is necessary.

# Writing `getCoords` functions

## Inputs

| Input | Description |
|------|-------------------------------------|
| `df` | Data frame of raw values |
| `cov` | Covariance matrix of data frame |
| `covinv` | Inverse covariance matrix of data frame |
| `exp` | reference point | 

## Ouput

The function should return a single array the same size of the input df and with the same column names as df.

## Example

```{r,eval=FALSE}
pullCoordsNoCov <- function(df, cov, exp, ...){

  n <- nrow(df)
  df <- as.matrix(df)
  nc <- ncol(df)
  coord_mat <- matrix(nrow = n, ncol = nc)

  for (i in 1:n){
    for (j in 1:nc){
      coord_mat[i, j] <- as.numeric((df[i, j] - exp$value[j]) / sqrt(cov[j, j]))
    }
  }
  colnames(coord_mat) <- colnames(df)
  return(coord_mat)
}

pandemonium(df,getCoords = list(pull = pullCoordsNoCov, normal = normCoords))

```


