goggles: View single cell dataset

In wjawaid/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, seed = 0, drl_options = NULL,
  filter.mean = 0.01, filter.cv = 2, use_fano = FALSE, verbose = FALSE,
  oldOut = NULL, repeatDRL = FALSE, ...)

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.
seed	Set seed to aid reproducibility
drl_options	Options passed to layout_with_drl()
filter.mean	Default 1e-02. Threshold for mean filter
filter.cv	Default 2. Threshold for CV/Fano filter
use_fano	Default FALSE. If TRUE use Fano factor not CV.
verbose	Default FALSE. If TRUE will return more details
oldOut	Default NULL. Can return previous results for quicker analysis.
repeatDRL	Default FALSE. If you wish to redo the layout using previous iteration layout as starting point.
...	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)

wjawaid/roots documentation built on Sept. 12, 2017, 9:51 a.m.