goggles: View single cell dataset

In roots: Reconstructing Ordered Ontogenic Trajectories

Description

View single cell dataset

Usage

goggles(x, pcaDims = 90, nsig = 5, dmat = NULL, mkv = NULL,
  plotDims = 2, kernSq = 2, ...)

Arguments

x	Matrix with cells in rows and gene in columns
pcaDims	Number of PCA dimensions to keep for distance measure
nsig	Number of significant neighbours to keep for Gaussian kernel
dmat	Optional. Give your own distance matrix
mkv	Optional. Give your own markov matrix.
plotDims	Default 2. Number of dimensions to plot
kernSq	Factor to tighten kernel - operates on sigmas.
...	Additonal parameters not currently in use

Details

View single cell dataset

Value

A list of l, dimensionality reduced data.frame; clust, returned from louvainClust(); adj, Sparse, pruned adjacency matrix; dmat, distance matrix; pca, PCA reduced matrix. sparse, diagnostics on adj prior to applying sparseMarkov().

Author(s)

Wajid Jawaid

Examples

## Not run: 
xx <- goggles(x)
plot(xx$l)

## End(Not run)

roots documentation built on May 2, 2019, 6:45 a.m.