goggles: View single cell dataset

Description Usage Arguments Details Value Author(s) Examples

View source: R/visualisation.r

Description

View single cell dataset

Usage

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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

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

## End(Not run)

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