Calculates the conditional probability of each cell belong to each cluster given all other cluster assignments

Calculates the conditional probability of each cell belong to each cluster given all other cluster assignments

# S3 method for celda_CG
clusterProbability(counts, celda.mod, log = FALSE, ...)

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 object of class "celda_CG".
log	Logical. If FALSE, then the normalized conditional probabilities will be returned. If TRUE, then the unnormalized log probabilities will be returned. Default FALSE.
...	Additional parameters.

Value

A list containging a matrix for the conditional cell and feature cluster probabilities.

Examples

celda.sim = simulateCells("celda_CG")
celda.mod = celda_CG(celda.sim$counts, K=celda.sim$K, L=celda.sim$L)
#> --------------------------------------------------------------------
#> Starting Celda_CG: Clustering cells and genes.
#> --------------------------------------------------------------------
#> Thu Sep 06 12:56:34 2018 .. Initializing chain 1 with 'random' (seed=12345)
#> Thu Sep 06 12:56:34 2018 .... Completed iteration: 1 | logLik: -1302242.28026966
#> Thu Sep 06 12:56:34 2018 .... Completed iteration: 2 | logLik: -1270044.02532694
#> Thu Sep 06 12:56:34 2018 .... Completed iteration: 3 | logLik: -1262209.15789703
#> Thu Sep 06 12:56:34 2018 .... Completed iteration: 4 | logLik: -1261712.35040107
#> Thu Sep 06 12:56:34 2018 .... Completed iteration: 5 | logLik: -1261712.57070977
#> Thu Sep 06 12:56:34 2018 .... Completed iteration: 6 | logLik: -1261711.00382116
#> Thu Sep 06 12:56:34 2018 .... Completed iteration: 7 | logLik: -1261716.24159949
#> Thu Sep 06 12:56:34 2018 .... Completed iteration: 8 | logLik: -1261479.73933942
#> Thu Sep 06 12:56:34 2018 .... Completed iteration: 9 | logLik: -1259874.14368698
#> Thu Sep 06 12:56:34 2018 .... Determining if any cell clusters should be split.
#> Thu Sep 06 12:56:34 2018 .... Cluster 1 was reassigned and cluster 4 was split in two.
#> Thu Sep 06 12:56:34 2018 .... Determining if any gene clusters should be split.
#> Thu Sep 06 12:56:35 2018 .... Cluster 2 was reassigned and cluster 9 was split in two.
#> Thu Sep 06 12:56:35 2018 .... Completed iteration: 10 | logLik: -1248355.63470669
#> Thu Sep 06 12:56:35 2018 .... Completed iteration: 11 | logLik: -1248355.63470669
#> Thu Sep 06 12:56:35 2018 .... Completed iteration: 12 | logLik: -1248355.63470669
#> Thu Sep 06 12:56:35 2018 .... Completed iteration: 13 | logLik: -1248355.63470669
#> Thu Sep 06 12:56:35 2018 .... Completed iteration: 14 | logLik: -1248355.63470669
#> Thu Sep 06 12:56:35 2018 .... Completed iteration: 15 | logLik: -1248355.63470669
#> Thu Sep 06 12:56:35 2018 .... Completed iteration: 16 | logLik: -1248355.63470669
#> Thu Sep 06 12:56:35 2018 .... Completed iteration: 17 | logLik: -1248355.63470669
#> Thu Sep 06 12:56:35 2018 .... Completed iteration: 18 | logLik: -1248355.63470669
#> Thu Sep 06 12:56:35 2018 .... Completed iteration: 19 | logLik: -1248355.63470669
#> Thu Sep 06 12:56:35 2018 .... Determining if any cell clusters should be split.
#> Thu Sep 06 12:56:35 2018 .... No additional splitting was performed.
#> Thu Sep 06 12:56:35 2018 .... Determining if any gene clusters should be split.
#> Thu Sep 06 12:56:36 2018 .... No additional splitting was performed.
#> Thu Sep 06 12:56:36 2018 .... Completed iteration: 20 | logLik: -1248355.63470669
#> Thu Sep 06 12:56:36 2018 .. Finished chain 1 with seed 12345
#> Thu Sep 06 12:56:36 2018 .. Initializing chain 2 with 'random' (seed=12346)
#> Thu Sep 06 12:56:36 2018 .... Completed iteration: 1 | logLik: -1288484.90567663
#> Thu Sep 06 12:56:36 2018 .... Completed iteration: 2 | logLik: -1252316.73202744
#> Thu Sep 06 12:56:36 2018 .... Completed iteration: 3 | logLik: -1250339.95568952
#> Thu Sep 06 12:56:36 2018 .... Completed iteration: 4 | logLik: -1249564.71677654
#> Thu Sep 06 12:56:36 2018 .... Completed iteration: 5 | logLik: -1249563.6294892
#> Thu Sep 06 12:56:36 2018 .... Completed iteration: 6 | logLik: -1249564.31589985
#> Thu Sep 06 12:56:36 2018 .... Completed iteration: 7 | logLik: -1249563.24732323
#> Thu Sep 06 12:56:36 2018 .... Completed iteration: 8 | logLik: -1249563.4198964
#> Thu Sep 06 12:56:36 2018 .... Completed iteration: 9 | logLik: -1249563.4198964
#> Thu Sep 06 12:56:36 2018 .... Determining if any cell clusters should be split.
#> Thu Sep 06 12:56:36 2018 .... No additional splitting was performed.
#> Thu Sep 06 12:56:36 2018 .... Determining if any gene clusters should be split.
#> Thu Sep 06 12:56:36 2018 .... Cluster 1 was reassigned and cluster 5 was split in two.
#> Thu Sep 06 12:56:36 2018 .... Completed iteration: 10 | logLik: -1248355.63470669
#> Thu Sep 06 12:56:36 2018 .... Completed iteration: 11 | logLik: -1248355.63470669
#> Thu Sep 06 12:56:36 2018 .... Completed iteration: 12 | logLik: -1248355.63470669
#> Thu Sep 06 12:56:37 2018 .... Completed iteration: 13 | logLik: -1248355.63470669
#> Thu Sep 06 12:56:37 2018 .... Completed iteration: 14 | logLik: -1248355.63470669
#> Thu Sep 06 12:56:37 2018 .... Completed iteration: 15 | logLik: -1248355.63470669
#> Thu Sep 06 12:56:37 2018 .... Completed iteration: 16 | logLik: -1248355.63470669
#> Thu Sep 06 12:56:37 2018 .... Completed iteration: 17 | logLik: -1248355.63470669
#> Thu Sep 06 12:56:37 2018 .... Completed iteration: 18 | logLik: -1248355.63470669
#> Thu Sep 06 12:56:37 2018 .... Completed iteration: 19 | logLik: -1248355.63470669
#> Thu Sep 06 12:56:37 2018 .... Determining if any cell clusters should be split.
#> Thu Sep 06 12:56:37 2018 .... No additional splitting was performed.
#> Thu Sep 06 12:56:37 2018 .... Determining if any gene clusters should be split.
#> Thu Sep 06 12:56:37 2018 .... No additional splitting was performed.
#> Thu Sep 06 12:56:37 2018 .... Completed iteration: 20 | logLik: -1248355.63470669
#> Thu Sep 06 12:56:37 2018 .. Finished chain 2 with seed 12346
#> Thu Sep 06 12:56:37 2018 .. Initializing chain 3 with 'random' (seed=12347)
#> Thu Sep 06 12:56:37 2018 .... Completed iteration: 1 | logLik: -1272446.65246189
#> Thu Sep 06 12:56:37 2018 .... Completed iteration: 2 | logLik: -1251530.86145074
#> Thu Sep 06 12:56:37 2018 .... Completed iteration: 3 | logLik: -1251528.38544994
#> Thu Sep 06 12:56:37 2018 .... Completed iteration: 4 | logLik: -1251523.68686302
#> Thu Sep 06 12:56:37 2018 .... Completed iteration: 5 | logLik: -1251527.44696783
#> Thu Sep 06 12:56:37 2018 .... Completed iteration: 6 | logLik: -1251522.13351871
#> Thu Sep 06 12:56:37 2018 .... Completed iteration: 7 | logLik: -1251526.73996701
#> Thu Sep 06 12:56:37 2018 .... Completed iteration: 8 | logLik: -1251529.06808316
#> Thu Sep 06 12:56:37 2018 .... Completed iteration: 9 | logLik: -1251527.40248727
#> Thu Sep 06 12:56:37 2018 .... Determining if any cell clusters should be split.
#> Thu Sep 06 12:56:37 2018 .... No additional splitting was performed.
#> Thu Sep 06 12:56:37 2018 .... Determining if any gene clusters should be split.
#> Thu Sep 06 12:56:38 2018 .... Cluster 1 was reassigned and cluster 5 was split in two.
#> Thu Sep 06 12:56:38 2018 .... Completed iteration: 10 | logLik: -1248422.30438372
#> Thu Sep 06 12:56:38 2018 .... Completed iteration: 11 | logLik: -1248355.63470669
#> Thu Sep 06 12:56:38 2018 .... Completed iteration: 12 | logLik: -1248355.63470669
#> Thu Sep 06 12:56:38 2018 .... Completed iteration: 13 | logLik: -1248355.63470669
#> Thu Sep 06 12:56:38 2018 .... Completed iteration: 14 | logLik: -1248355.63470669
#> Thu Sep 06 12:56:38 2018 .... Completed iteration: 15 | logLik: -1248355.63470669
#> Thu Sep 06 12:56:38 2018 .... Completed iteration: 16 | logLik: -1248355.63470669
#> Thu Sep 06 12:56:38 2018 .... Completed iteration: 17 | logLik: -1248355.63470669
#> Thu Sep 06 12:56:38 2018 .... Completed iteration: 18 | logLik: -1248355.63470669
#> Thu Sep 06 12:56:38 2018 .... Completed iteration: 19 | logLik: -1248355.63470669
#> Thu Sep 06 12:56:38 2018 .... Determining if any gene clusters should be split.
#> Thu Sep 06 12:56:38 2018 .... No additional splitting was performed.
#> Thu Sep 06 12:56:38 2018 .... Completed iteration: 20 | logLik: -1248355.63470669
#> Thu Sep 06 12:56:38 2018 .... Determining if any cell clusters should be split.
#> Thu Sep 06 12:56:38 2018 .... No additional splitting was performed.
#> Thu Sep 06 12:56:38 2018 .... Determining if any gene clusters should be split.
#> Thu Sep 06 12:56:39 2018 .... No additional splitting was performed.
#> Thu Sep 06 12:56:39 2018 .... Completed iteration: 21 | logLik: -1248355.63470669
#> Thu Sep 06 12:56:39 2018 .. Finished chain 3 with seed 12347
#> --------------------------------------------------------------------
#> Completed Celda_CG. Total time: 4.773285 secs
#> --------------------------------------------------------------------
cluster.prob = clusterProbability(celda.sim$counts, celda.mod)