celdaHeatmap.celda_CG.Rd
celdaHeatmap for celda Cell and Gene clustering model.
# S3 method for celda_CG celdaHeatmap(counts, celda.mod, nfeatures = 25, ...)
counts | Integer matrix. Rows represent features and columns represent cells. This matrix should be the same as the one used to generate `celda.mod`. |
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celda.mod | Celda object of class "celda_CG". |
nfeatures | Integer. Maximum number of features to select for each module. Default 25. |
... | Additional parameters. |
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 12:55:20 2018 .. Initializing chain 1 with 'random' (seed=12345)#> Thu Sep 06 12:55:20 2018 .... Completed iteration: 1 | logLik: -1302242.28026966#> Thu Sep 06 12:55:20 2018 .... Completed iteration: 2 | logLik: -1270044.02532694#> Thu Sep 06 12:55:20 2018 .... Completed iteration: 3 | logLik: -1262209.15789703#> Thu Sep 06 12:55:20 2018 .... Completed iteration: 4 | logLik: -1261712.35040107#> Thu Sep 06 12:55:20 2018 .... Completed iteration: 5 | logLik: -1261712.57070977#> Thu Sep 06 12:55:20 2018 .... Completed iteration: 6 | logLik: -1261711.00382116#> Thu Sep 06 12:55:20 2018 .... Completed iteration: 7 | logLik: -1261716.24159949#> Thu Sep 06 12:55:20 2018 .... Completed iteration: 8 | logLik: -1261479.73933942#> Thu Sep 06 12:55:20 2018 .... Completed iteration: 9 | logLik: -1259874.14368698#> Thu Sep 06 12:55:20 2018 .... Determining if any cell clusters should be split.#> Thu Sep 06 12:55:20 2018 .... Cluster 1 was reassigned and cluster 4 was split in two.#> Thu Sep 06 12:55:20 2018 .... Determining if any gene clusters should be split.#> Thu Sep 06 12:55:21 2018 .... Cluster 2 was reassigned and cluster 9 was split in two.#> Thu Sep 06 12:55:21 2018 .... Completed iteration: 10 | logLik: -1248355.63470669#> Thu Sep 06 12:55:21 2018 .... Completed iteration: 11 | logLik: -1248355.63470669#> Thu Sep 06 12:55:21 2018 .... Completed iteration: 12 | logLik: -1248355.63470669#> Thu Sep 06 12:55:21 2018 .... Completed iteration: 13 | logLik: -1248355.63470669#> Thu Sep 06 12:55:21 2018 .... Completed iteration: 14 | logLik: -1248355.63470669#> Thu Sep 06 12:55:21 2018 .... Completed iteration: 15 | logLik: -1248355.63470669#> Thu Sep 06 12:55:21 2018 .... Completed iteration: 16 | logLik: -1248355.63470669#> Thu Sep 06 12:55:21 2018 .... Completed iteration: 17 | logLik: -1248355.63470669#> Thu Sep 06 12:55:21 2018 .... Completed iteration: 18 | logLik: -1248355.63470669#> Thu Sep 06 12:55:21 2018 .... Completed iteration: 19 | logLik: -1248355.63470669#> Thu Sep 06 12:55:21 2018 .... Determining if any cell clusters should be split.#> Thu Sep 06 12:55:22 2018 .... No additional splitting was performed.#> Thu Sep 06 12:55:22 2018 .... Determining if any gene clusters should be split.#> Thu Sep 06 12:55:22 2018 .... No additional splitting was performed.#> Thu Sep 06 12:55:22 2018 .... Completed iteration: 20 | logLik: -1248355.63470669#> Thu Sep 06 12:55:22 2018 .. Finished chain 1 with seed 12345#> Thu Sep 06 12:55:22 2018 .. Initializing chain 2 with 'random' (seed=12346)#> Thu Sep 06 12:55:22 2018 .... Completed iteration: 1 | logLik: -1288484.90567663#> Thu Sep 06 12:55:22 2018 .... Completed iteration: 2 | logLik: -1252316.73202744#> Thu Sep 06 12:55:22 2018 .... Completed iteration: 3 | logLik: -1250339.95568952#> Thu Sep 06 12:55:22 2018 .... Completed iteration: 4 | logLik: -1249564.71677654#> Thu Sep 06 12:55:22 2018 .... Completed iteration: 5 | logLik: -1249563.6294892#> Thu Sep 06 12:55:22 2018 .... Completed iteration: 6 | logLik: -1249564.31589985#> Thu Sep 06 12:55:22 2018 .... Completed iteration: 7 | logLik: -1249563.24732323#> Thu Sep 06 12:55:22 2018 .... Completed iteration: 8 | logLik: -1249563.4198964#> Thu Sep 06 12:55:22 2018 .... Completed iteration: 9 | logLik: -1249563.4198964#> Thu Sep 06 12:55:23 2018 .... Determining if any cell clusters should be split.#> Thu Sep 06 12:55:23 2018 .... No additional splitting was performed.#> Thu Sep 06 12:55:23 2018 .... Determining if any gene clusters should be split.#> Thu Sep 06 12:55:23 2018 .... Cluster 1 was reassigned and cluster 5 was split in two.#> Thu Sep 06 12:55:23 2018 .... Completed iteration: 10 | logLik: -1248355.63470669#> Thu Sep 06 12:55:23 2018 .... Completed iteration: 11 | logLik: -1248355.63470669#> Thu Sep 06 12:55:23 2018 .... Completed iteration: 12 | logLik: -1248355.63470669#> Thu Sep 06 12:55:23 2018 .... Completed iteration: 13 | logLik: -1248355.63470669#> Thu Sep 06 12:55:23 2018 .... Completed iteration: 14 | logLik: -1248355.63470669#> Thu Sep 06 12:55:24 2018 .... Completed iteration: 15 | logLik: -1248355.63470669#> Thu Sep 06 12:55:24 2018 .... Completed iteration: 16 | logLik: -1248355.63470669#> Thu Sep 06 12:55:24 2018 .... Completed iteration: 17 | logLik: -1248355.63470669#> Thu Sep 06 12:55:24 2018 .... Completed iteration: 18 | logLik: -1248355.63470669#> Thu Sep 06 12:55:24 2018 .... Completed iteration: 19 | logLik: -1248355.63470669#> Thu Sep 06 12:55:24 2018 .... Determining if any cell clusters should be split.#> Thu Sep 06 12:55:24 2018 .... No additional splitting was performed.#> Thu Sep 06 12:55:24 2018 .... Determining if any gene clusters should be split.#> Thu Sep 06 12:55:25 2018 .... No additional splitting was performed.#> Thu Sep 06 12:55:25 2018 .... Completed iteration: 20 | logLik: -1248355.63470669#> Thu Sep 06 12:55:25 2018 .. Finished chain 2 with seed 12346#> Thu Sep 06 12:55:25 2018 .. Initializing chain 3 with 'random' (seed=12347)#> Thu Sep 06 12:55:25 2018 .... Completed iteration: 1 | logLik: -1272446.65246189#> Thu Sep 06 12:55:25 2018 .... Completed iteration: 2 | logLik: -1251530.86145074#> Thu Sep 06 12:55:25 2018 .... Completed iteration: 3 | logLik: -1251528.38544994#> Thu Sep 06 12:55:25 2018 .... Completed iteration: 4 | logLik: -1251523.68686302#> Thu Sep 06 12:55:25 2018 .... Completed iteration: 5 | logLik: -1251527.44696783#> Thu Sep 06 12:55:25 2018 .... Completed iteration: 6 | logLik: -1251522.13351871#> Thu Sep 06 12:55:25 2018 .... Completed iteration: 7 | logLik: -1251526.73996701#> Thu Sep 06 12:55:25 2018 .... Completed iteration: 8 | logLik: -1251529.06808316#> Thu Sep 06 12:55:25 2018 .... Completed iteration: 9 | logLik: -1251527.40248727#> Thu Sep 06 12:55:25 2018 .... Determining if any cell clusters should be split.#> Thu Sep 06 12:55:25 2018 .... No additional splitting was performed.#> Thu Sep 06 12:55:25 2018 .... Determining if any gene clusters should be split.#> Thu Sep 06 12:55:26 2018 .... Cluster 1 was reassigned and cluster 5 was split in two.#> Thu Sep 06 12:55:26 2018 .... Completed iteration: 10 | logLik: -1248422.30438372#> Thu Sep 06 12:55:26 2018 .... Completed iteration: 11 | logLik: -1248355.63470669#> Thu Sep 06 12:55:26 2018 .... Completed iteration: 12 | logLik: -1248355.63470669#> Thu Sep 06 12:55:26 2018 .... Completed iteration: 13 | logLik: -1248355.63470669#> Thu Sep 06 12:55:26 2018 .... Completed iteration: 14 | logLik: -1248355.63470669#> Thu Sep 06 12:55:26 2018 .... Completed iteration: 15 | logLik: -1248355.63470669#> Thu Sep 06 12:55:26 2018 .... Completed iteration: 16 | logLik: -1248355.63470669#> Thu Sep 06 12:55:26 2018 .... Completed iteration: 17 | logLik: -1248355.63470669#> Thu Sep 06 12:55:26 2018 .... Completed iteration: 18 | logLik: -1248355.63470669#> Thu Sep 06 12:55:26 2018 .... Completed iteration: 19 | logLik: -1248355.63470669#> Thu Sep 06 12:55:26 2018 .... Determining if any gene clusters should be split.#> Thu Sep 06 12:55:27 2018 .... No additional splitting was performed.#> Thu Sep 06 12:55:27 2018 .... Completed iteration: 20 | logLik: -1248355.63470669#> Thu Sep 06 12:55:27 2018 .... Determining if any cell clusters should be split.#> Thu Sep 06 12:55:27 2018 .... No additional splitting was performed.#> Thu Sep 06 12:55:27 2018 .... Determining if any gene clusters should be split.#> Thu Sep 06 12:55:27 2018 .... No additional splitting was performed.#> Thu Sep 06 12:55:27 2018 .... Completed iteration: 21 | logLik: -1248355.63470669#> Thu Sep 06 12:55:27 2018 .. Finished chain 3 with seed 12347#> --------------------------------------------------------------------#> Completed Celda_CG. Total time: 7.57766 secs#> --------------------------------------------------------------------