# Understanding the dimReduction Function Input

# Overview

This vignette describes the usage of the `dimReduction` parameter in the `pandemonium` app and how new functions can be written for it.

The input for `dimReduction` should be a named list of functions, where each function defines a dimension reduction and needs to be structured as follows.

## Required function inputs:

`mat` = n x m matrix of coordinates to reduce `dist` = n x n distance matrix

While typically only one of the two is used for the dimension reduction, the interface requires that both arguments are accepted to avoid errors.

## What the function should return:

A list object that contains the output of the dimension reduction and can be accessed as `dimReduction(mat = mat, dist = dist)$Y` = n x 2 matrix or data frame with dimension reduced coordinates for all observations.

# How to write new functions

The standard way to write a new function to be passed to `dimReduction` is as a wrapper for a common dimension reduction algorithm. The defined function must be able to take `mat` and `dist` as parameters. If only one of them is used it is best to write the function with space for additional parameters with `...` as seen in the following example.

    tSNE_mat <- function(mat,...) {
      coord_red = list()
      coord_red$Y = Rtsne::Rtsne(mat)$Y
      coord_red
    }

    tSNE_dist <- function(dist,...) {
      coord_red = list()
      coord_red$Y = Rtsne::Rtsne(dist, is.dist = TRUE)$Y
      coord_red
    }

    newPandemonium(df, dim_reduction = list(tSNE_mat = tSNE_mat, tSNE_dist = tSNE_dist))

Some algorithms may take a dist object instead of a distance matrix. This can be done by converting the distance matrix using `stats::as.dist()`. An example is the implementation of `umap`.

    umap <- function(dist,...) {
      ret <- list()
      ret$Y <- uwot::umap(stats::as.dist(dist))
      ret
    }

    newPandemonium(df, dim_reduction = list(umap = umap))