goggles {roots} | R Documentation |
View single cell dataset
goggles(x, pcaDims = 90, nsig = 5, dmat = NULL, mkv = NULL,
plotDims = 2, kernSq = 2, ...)
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 |
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
## Not run:
xx <- goggles(x)
plot(xx$l)
## End(Not run)