celdaHeatmap for celda Cell clustering function

celdaHeatmap for celda Cell clustering function

# S3 method for celda_C
celdaHeatmap(counts, celda.mod, feature.ix, ...)

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_C".
feature.ix	Integer vector. Indices of features to plot, such the top features from a differential expression analysis.
...	Additional parameters.

Examples

celda.sim = simulateCells("celda_C")
celda.mod = celda_C(celda.sim$counts, K=celda.sim$K)
#> --------------------------------------------------------------------
#> Starting Celda_C: Clustering cells.
#> --------------------------------------------------------------------
#> Thu Sep 06 12:55:15 2018 .. Initializing chain 1 with 'random' (seed=12345)
#> Thu Sep 06 12:55:15 2018 .... Completed iteration: 1 | logLik: -1403838.03777873
#> Thu Sep 06 12:55:15 2018 .... Completed iteration: 2 | logLik: -1400194.39761642
#> Thu Sep 06 12:55:15 2018 .... Completed iteration: 3 | logLik: -1377050.9603928
#> Thu Sep 06 12:55:15 2018 .... Completed iteration: 4 | logLik: -1377050.9603928
#> Thu Sep 06 12:55:15 2018 .... Completed iteration: 5 | logLik: -1377050.9603928
#> Thu Sep 06 12:55:15 2018 .... Completed iteration: 6 | logLik: -1377050.9603928
#> Thu Sep 06 12:55:15 2018 .... Completed iteration: 7 | logLik: -1377050.9603928
#> Thu Sep 06 12:55:15 2018 .... Completed iteration: 8 | logLik: -1377050.9603928
#> Thu Sep 06 12:55:15 2018 .... Completed iteration: 9 | logLik: -1377050.9603928
#> Thu Sep 06 12:55:15 2018 .... Determining if any cell clusters should be split.
#> Thu Sep 06 12:55:15 2018 .... Cluster 1 was reassigned and cluster 4 was split in two.
#> Thu Sep 06 12:55:15 2018 .... Completed iteration: 10 | logLik: -1358078.99551138
#> Thu Sep 06 12:55:15 2018 .... Completed iteration: 11 | logLik: -1358078.99551138
#> Thu Sep 06 12:55:15 2018 .... Completed iteration: 12 | logLik: -1358078.99551138
#> Thu Sep 06 12:55:15 2018 .... Completed iteration: 13 | logLik: -1358078.99551138
#> Thu Sep 06 12:55:15 2018 .... Completed iteration: 14 | logLik: -1358078.99551138
#> Thu Sep 06 12:55:15 2018 .... Completed iteration: 15 | logLik: -1358078.99551138
#> Thu Sep 06 12:55:15 2018 .... Completed iteration: 16 | logLik: -1358078.99551138
#> Thu Sep 06 12:55:15 2018 .... Completed iteration: 17 | logLik: -1358078.99551138
#> Thu Sep 06 12:55:15 2018 .... Completed iteration: 18 | logLik: -1358078.99551138
#> Thu Sep 06 12:55:15 2018 .... Completed iteration: 19 | logLik: -1358078.99551138
#> Thu Sep 06 12:55:15 2018 .... Determining if any cell clusters should be split.
#> Thu Sep 06 12:55:16 2018 .... No additional splitting was performed.
#> Thu Sep 06 12:55:16 2018 .... Completed iteration: 20 | logLik: -1358078.99551138
#> Thu Sep 06 12:55:16 2018 .. Finished chain 1 with seed 12345
#> Thu Sep 06 12:55:16 2018 .. Initializing chain 2 with 'random' (seed=12346)
#> Thu Sep 06 12:55:16 2018 .... Completed iteration: 1 | logLik: -1383993.83150535
#> Thu Sep 06 12:55:16 2018 .... Completed iteration: 2 | logLik: -1358078.99551138
#> Thu Sep 06 12:55:16 2018 .... Completed iteration: 3 | logLik: -1358078.99551138
#> Thu Sep 06 12:55:16 2018 .... Completed iteration: 4 | logLik: -1358078.99551138
#> Thu Sep 06 12:55:16 2018 .... Completed iteration: 5 | logLik: -1358078.99551138
#> Thu Sep 06 12:55:16 2018 .... Completed iteration: 6 | logLik: -1358078.99551138
#> Thu Sep 06 12:55:16 2018 .... Completed iteration: 7 | logLik: -1358078.99551138
#> Thu Sep 06 12:55:16 2018 .... Completed iteration: 8 | logLik: -1358078.99551138
#> Thu Sep 06 12:55:16 2018 .... Completed iteration: 9 | logLik: -1358078.99551138
#> Thu Sep 06 12:55:16 2018 .... Determining if any cell clusters should be split.
#> Thu Sep 06 12:55:16 2018 .... No additional splitting was performed.
#> Thu Sep 06 12:55:16 2018 .... Completed iteration: 10 | logLik: -1358078.99551138
#> Thu Sep 06 12:55:16 2018 .... Completed iteration: 11 | logLik: -1358078.99551138
#> Thu Sep 06 12:55:16 2018 .... Determining if any cell clusters should be split.
#> Thu Sep 06 12:55:16 2018 .... No additional splitting was performed.
#> Thu Sep 06 12:55:16 2018 .... Completed iteration: 12 | logLik: -1358078.99551138
#> Thu Sep 06 12:55:16 2018 .. Finished chain 2 with seed 12346
#> Thu Sep 06 12:55:16 2018 .. Initializing chain 3 with 'random' (seed=12347)
#> Thu Sep 06 12:55:16 2018 .... Completed iteration: 1 | logLik: -1358078.99551138
#> Thu Sep 06 12:55:16 2018 .... Completed iteration: 2 | logLik: -1358078.99551138
#> Thu Sep 06 12:55:16 2018 .... Completed iteration: 3 | logLik: -1358078.99551138
#> Thu Sep 06 12:55:16 2018 .... Completed iteration: 4 | logLik: -1358078.99551138
#> Thu Sep 06 12:55:16 2018 .... Completed iteration: 5 | logLik: -1358078.99551138
#> Thu Sep 06 12:55:16 2018 .... Completed iteration: 6 | logLik: -1358078.99551138
#> Thu Sep 06 12:55:16 2018 .... Completed iteration: 7 | logLik: -1358078.99551138
#> Thu Sep 06 12:55:16 2018 .... Completed iteration: 8 | logLik: -1358078.99551138
#> Thu Sep 06 12:55:16 2018 .... Completed iteration: 9 | logLik: -1358078.99551138
#> Thu Sep 06 12:55:16 2018 .... Determining if any cell clusters should be split.
#> Thu Sep 06 12:55:17 2018 .... No additional splitting was performed.
#> Thu Sep 06 12:55:17 2018 .... Completed iteration: 10 | logLik: -1358078.99551138
#> Thu Sep 06 12:55:17 2018 .... Determining if any cell clusters should be split.
#> Thu Sep 06 12:55:17 2018 .... No additional splitting was performed.
#> Thu Sep 06 12:55:17 2018 .... Completed iteration: 11 | logLik: -1358078.99551138
#> Thu Sep 06 12:55:17 2018 .. Finished chain 3 with seed 12347
#> --------------------------------------------------------------------
#> Completed Celda_C. Total time: 1.649034 secs
#> --------------------------------------------------------------------
celdaHeatmap(celda.sim$counts, celda.mod)