knnDenoise {langevitour}

k-nearest neighbor denoising of a set of points

Description

Reduce noise in a high-dimensional dataset by averaging each point with its nearby neighbors.

Usage

knnDenoise(X, block = rep(1, nrow(X)), k = 30, steps = 2)

Arguments

X

A matrix of numeric data, or something that can be cast to a matrix. Each row represents a point.

block

Optional. A block for each row in X. A factor, or something that can be cast to a factor. Denoising will be performed independently within each block.

k

Number of nearest neighbors to find around each point (including itself).

steps

Number of steps to take along the directed k-nearest neighbor graph. steps=1 uses the k-nearest neighbors, steps=2 uses the k-nearest neighbors and their k-nearest neighbors, etc.

Details

knnDenoise first finds the k-nearest neighbors to each point (including the point itself). Then, for each point, the average is found of the points reachable in steps steps along the directed k-nearest neighbor graph.

Examples

library(palmerpenguins)

completePenguins <- na.omit(penguins[,c(1,3,4,5,6)])

# Dimensions need to be on comparable scales to apply knnDenoise
scaled <- scale(completePenguins[,-1])

denoised <- knnDenoise(scaled)

langevitour(denoised, completePenguins$species, pointSize=2)