JaccardSimTransform: A function that calculates a transformed Jaccard similarity...

In arh2207/APJaccard: Functions that assist using Jaccard similarity with AP clustering

A function that calculates a transformed Jaccard similarity matrix for the cells in a Seurat object. tanh with k=280 performed the best (outperformed Louvain) in one example with an annotated data set.

Description

A function that calculates a transformed Jaccard similarity matrix for the cells in a Seurat object. tanh with k=280 performed the best (outperformed Louvain) in one example with an annotated data set.

Usage

JaccardSimTransform(data.dist, k = 5, transformation = "default")

Arguments

data.dist	a distance matrix on which to use FindNeighbors
k	an integer representing the number of neighbors which will be found for each cell
transformation	a character vector indicating the type of transformation the similarity matrix will go through before being returned. By default the similarity matrix will be returned with no transformation. Other possible values include log (returns matrix which has been log transformed), 'inverse' returns a shifted inverse of the matrix, 'stretch' returns a linear scaling of the matrix, 'tan' returns the tangent of matrix values, and 'tanh' returns the hyperbolic tangent of matrix values

Value

an NxN matrix where N is the number of cells, and the matrix contains the transformed Jaccard values for all pairs of cells

arh2207/APJaccard documentation built on May 19, 2022, 11:59 p.m.