goggles {roots}

View single cell dataset

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)