embeddr: Laplacian eigenmaps embedding of single-cell RNA-seq data.

In kieranrcampbell/embeddr: Laplacian eigenmaps & principal curves for pseudotemporal ordering of single-cell RNA-seq data

Description

Laplacian eigenmaps embedding of single-cell RNA-seq data.

Usage

embeddr(sce, genes_for_embedding = NULL, kernel = c("nn", "dist", "heat"),
  metric = c("correlation", "euclidean", "cosine"),
  nn = round(log(ncol(sce))), eps = NULL, t = NULL,
  symmetrize = c("mean", "ceil", "floor"), measure_type = c("unorm",
  "norm"), p = 2)

Arguments

sce	The SCESet object
genes_for_embedding	A vector of gene indices or names to subset the sce for the embedding. The returned object contains the full original gene set found in sce.
kernel	The choice of kernel. 'nn' will give nearest neighbours, 'dist' gives minimum distance and 'heat' gives a heat kernel. Discussed in detail in 'Laplacian Eigenmaps and Spectral Techniques for Embedding and Clustering', Belkin & Niyogi
metric	The metric with which to assess 'closeness' for nearest neighbour selection, one of 'correlation' (pearson) or 'euclidean'. Default is 'correlation'.
nn	Number of nearest neighbours if kernel == 'nn'
eps	Maximum distance parameter if kernel == 'dist'
t	'time' for heat kernel if kernel == 'heat'
symmetrize	How to make the adjacency matrix symmetric. Note that slightly counterintuitively, node i having node j as a nearest neighbour doesn't guarantee node j has node i. There are several ways to get round this: mean If the above case occurs make the link weight 0.5 so the adjacency matrix becomes 0.5(A + A') ceil If the above case occurs set the link weight to 1 (ie take the ceiling of the mean case) floor If the above case occurs set the link weight to 0 (ie take the floor of the mean case)
measure_type	Type of laplacian eigenmap, which corresponds to the constraint on the eigenvalue problem. If type is 'unorm' (default), then the graph measure used is the identity matrix, while if type is 'norm' then the measure used is the degree matrix.
p	Dimension of the embedded space, default is 2

Value

An object of class SCESet

Examples

library(scater)
data('sc_example_counts') ; sce <- newSCESet(countData = sc_example_counts)
sce <- embeddr(sce)

kieranrcampbell/embeddr documentation built on May 20, 2019, 9:24 a.m.