Embeds cells in two dimensions using tSNE based on celda_CG results.

Embeds cells in two dimensions using tSNE based on celda_CG results.

celdaTsne(counts, celda.mod, ...)

Arguments

counts	Integer matrix. Rows represent features and columns represent cells. This matrix should be the same as the one used to generate `celda.mod`.
celda.mod	Celda model. Options available in `celda::available.models`.
...	Additional parameters.

Value

Numeric Matrix of dimension `ncol(counts)` x 2, colums representing the "X" and "Y" coordinates in the data's t-SNE represetation.

Examples

celda.sim = simulateCells("celda_CG")
celda.mod = celda_CG(celda.sim$counts, K=celda.sim$K, L=celda.sim$L,
                     nchains=1, max.iter=1)
#> --------------------------------------------------------------------
#> Starting Celda_CG: Clustering cells and genes.
#> --------------------------------------------------------------------
#> Thu Sep 06 12:56:17 2018 .. Initializing chain 1 with 'random' (seed=12345)
#> Thu Sep 06 12:56:17 2018 .... Determining if any cell clusters should be split.
#> Thu Sep 06 12:56:17 2018 .... Cluster 4 was reassigned and cluster 3 was split in two.
#> Thu Sep 06 12:56:17 2018 .... Determining if any gene clusters should be split.
#> Thu Sep 06 12:56:17 2018 .... Cluster 2 was reassigned and cluster 9 was split in two.
#> Thu Sep 06 12:56:17 2018 .... Completed iteration: 1 | logLik: -1272652.93151523
#> Thu Sep 06 12:56:17 2018 .. Finished chain 1 with seed 12345
#> --------------------------------------------------------------------
#> Completed Celda_CG. Total time: 0.565676 secs
#> --------------------------------------------------------------------
tsne.res = celdaTsne(celda.sim$counts, celda.mod)