Description Usage Arguments Details Value Author(s) Examples
View source: R/visualisation.r
View single cell dataset
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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 |
View single cell dataset
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().
Wajid Jawaid
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