buildWijMatrix: Rescale the weights in an edge matrix to match a given...

In pagoda2: Single Cell Analysis and Differential Expression

Rescale the weights in an edge matrix to match a given perplexity. From 'largeVis', <https://github.com/elbamos/largeVis>

Description

Rescale the weights in an edge matrix to match a given perplexity. From 'largeVis', <https://github.com/elbamos/largeVis>

Usage

buildWijMatrix(x, threads = NULL, perplexity = 50)

Arguments

x	An edgematrix, either an 'edgematrix' object or a sparse matrix.
threads	numeric The maximum number of threads to spawn (default=NULL). Determined automatically if NULL (default=NULL)
perplexity	numeric Given perplexity (default=50)

Value

A list with the following components:

'dist'

An [N,K] matrix of the distances to the nearest neighbors.

'id'

An [N,K] matrix of the node indexes of the neartest neighbors. Note that this matrix is 1-indexed, unlike most other matrices in this package.

'k'

The number of nearest neighbors.

pagoda2 documentation built on June 24, 2024, 9:09 a.m.