Create a scatterplot based on celda cluster labels.

Create a scatterplot based on celda cluster labels.

plotDimReduceCluster(dim1, dim2, cluster, size = 1, xlab = "Dimension_1",
  ylab = "Dimension_2", specific_clusters = NULL)

Arguments

dim1

Numeric vector. First dimension from data dimensionality reduction output.
dim2

Numeric vector. Second dimension from data dimensionality reduction output.
cluster

Integer vector. Contains cluster labels for each cell.
size

Numeric. Sets size of point on plot. Default 1.
xlab

Character vector. Label for the x-axis. Default "Dimension_1".
ylab

Character vector. Label for the y-axis. Default "Dimension_2".
specific_clusters

Numeric vector. Only color cells in the specified clusters. All other cells will be grey. If NULL, all clusters will be colored. Default NULL.

Examples

sim.res = simulateCells(model="celda_CG", K = 5, L = 5)
celda_cg <- celda_CG(counts = sim.res$counts, K = 5, L = 5)
#> --------------------------------------------------------------------
#> Starting Celda_CG: Clustering cells and genes.
#> --------------------------------------------------------------------
#> Thu Sep 06 12:57:24 2018 .. Initializing chain 1 with 'random' (seed=12345)
#> Thu Sep 06 12:57:24 2018 .... Completed iteration: 1 | logLik: -1292432.99348905
#> Thu Sep 06 12:57:24 2018 .... Completed iteration: 2 | logLik: -1271152.8119707
#> Thu Sep 06 12:57:25 2018 .... Completed iteration: 3 | logLik: -1271146.08792976
#> Thu Sep 06 12:57:25 2018 .... Completed iteration: 4 | logLik: -1271142.13405322
#> Thu Sep 06 12:57:25 2018 .... Completed iteration: 5 | logLik: -1271138.7926281
#> Thu Sep 06 12:57:25 2018 .... Completed iteration: 6 | logLik: -1271139.37518801
#> Thu Sep 06 12:57:25 2018 .... Completed iteration: 7 | logLik: -1271135.02027059
#> Thu Sep 06 12:57:25 2018 .... Completed iteration: 8 | logLik: -1271133.69255723
#> Thu Sep 06 12:57:25 2018 .... Completed iteration: 9 | logLik: -1271131.24555386
#> Thu Sep 06 12:57:25 2018 .... Determining if any cell clusters should be split.
#> Thu Sep 06 12:57:25 2018 .... Cluster 1 was reassigned and cluster 3 was split in two.
#> Thu Sep 06 12:57:25 2018 .... Determining if any gene clusters should be split.
#> Thu Sep 06 12:57:25 2018 .... No additional splitting was performed.
#> Thu Sep 06 12:57:25 2018 .... Completed iteration: 10 | logLik: -1265977.81160925
#> Thu Sep 06 12:57:25 2018 .... Completed iteration: 11 | logLik: -1265977.81160925
#> Thu Sep 06 12:57:25 2018 .... Completed iteration: 12 | logLik: -1265977.42998371
#> Thu Sep 06 12:57:25 2018 .... Completed iteration: 13 | logLik: -1265977.81160925
#> Thu Sep 06 12:57:25 2018 .... Completed iteration: 14 | logLik: -1265977.42998371
#> Thu Sep 06 12:57:25 2018 .... Completed iteration: 15 | logLik: -1265977.42998371
#> Thu Sep 06 12:57:25 2018 .... Completed iteration: 16 | logLik: -1265977.42998371
#> Thu Sep 06 12:57:25 2018 .... Completed iteration: 17 | logLik: -1265977.81160925
#> Thu Sep 06 12:57:25 2018 .... Completed iteration: 18 | logLik: -1265977.42998371
#> Thu Sep 06 12:57:25 2018 .... Completed iteration: 19 | logLik: -1265977.42998371
#> Thu Sep 06 12:57:25 2018 .... Determining if any cell clusters should be split.
#> Thu Sep 06 12:57:26 2018 .... No additional splitting was performed.
#> Thu Sep 06 12:57:26 2018 .... Completed iteration: 20 | logLik: -1265977.42998371
#> Thu Sep 06 12:57:26 2018 .... Completed iteration: 21 | logLik: -1265977.81160925
#> Thu Sep 06 12:57:26 2018 .... Determining if any cell clusters should be split.
#> Thu Sep 06 12:57:26 2018 .... No additional splitting was performed.
#> Thu Sep 06 12:57:26 2018 .... Determining if any gene clusters should be split.
#> Thu Sep 06 12:57:26 2018 .... No additional splitting was performed.
#> Thu Sep 06 12:57:26 2018 .... Completed iteration: 22 | logLik: -1265977.81160925
#> Thu Sep 06 12:57:26 2018 .. Finished chain 1 with seed 12345
#> Thu Sep 06 12:57:26 2018 .. Initializing chain 2 with 'random' (seed=12346)
#> Thu Sep 06 12:57:26 2018 .... Completed iteration: 1 | logLik: -1296147.64459921
#> Thu Sep 06 12:57:26 2018 .... Completed iteration: 2 | logLik: -1273614.61367925
#> Thu Sep 06 12:57:27 2018 .... Completed iteration: 3 | logLik: -1271640.01823375
#> Thu Sep 06 12:57:27 2018 .... Completed iteration: 4 | logLik: -1271150.85741638
#> Thu Sep 06 12:57:27 2018 .... Completed iteration: 5 | logLik: -1270826.33540845
#> Thu Sep 06 12:57:27 2018 .... Completed iteration: 6 | logLik: -1268220.93677393
#> Thu Sep 06 12:57:27 2018 .... Completed iteration: 7 | logLik: -1265977.42998371
#> Thu Sep 06 12:57:27 2018 .... Completed iteration: 8 | logLik: -1265977.81160925
#> Thu Sep 06 12:57:27 2018 .... Completed iteration: 9 | logLik: -1265981.10028326
#> Thu Sep 06 12:57:27 2018 .... Determining if any cell clusters should be split.
#> Thu Sep 06 12:57:27 2018 .... No additional splitting was performed.
#> Thu Sep 06 12:57:27 2018 .... Determining if any gene clusters should be split.
#> Thu Sep 06 12:57:27 2018 .... No additional splitting was performed.
#> Thu Sep 06 12:57:27 2018 .... Completed iteration: 10 | logLik: -1265977.42998371
#> Thu Sep 06 12:57:27 2018 .... Completed iteration: 11 | logLik: -1265977.81160925
#> Thu Sep 06 12:57:27 2018 .... Completed iteration: 12 | logLik: -1265977.42998371
#> Thu Sep 06 12:57:27 2018 .... Completed iteration: 13 | logLik: -1265977.81160925
#> Thu Sep 06 12:57:27 2018 .... Completed iteration: 14 | logLik: -1265977.81160925
#> Thu Sep 06 12:57:27 2018 .... Completed iteration: 15 | logLik: -1265977.81160925
#> Thu Sep 06 12:57:27 2018 .... Completed iteration: 16 | logLik: -1265977.42998371
#> Thu Sep 06 12:57:27 2018 .... Determining if any cell clusters should be split.
#> Thu Sep 06 12:57:27 2018 .... No additional splitting was performed.
#> Thu Sep 06 12:57:27 2018 .... Determining if any gene clusters should be split.
#> Thu Sep 06 12:57:28 2018 .... No additional splitting was performed.
#> Thu Sep 06 12:57:28 2018 .... Completed iteration: 17 | logLik: -1265977.42998371
#> Thu Sep 06 12:57:28 2018 .. Finished chain 2 with seed 12346
#> Thu Sep 06 12:57:28 2018 .. Initializing chain 3 with 'random' (seed=12347)
#> Thu Sep 06 12:57:28 2018 .... Completed iteration: 1 | logLik: -1298276.1895605
#> Thu Sep 06 12:57:28 2018 .... Completed iteration: 2 | logLik: -1270053.97340606
#> Thu Sep 06 12:57:28 2018 .... Completed iteration: 3 | logLik: -1266751.51933782
#> Thu Sep 06 12:57:28 2018 .... Completed iteration: 4 | logLik: -1265977.42998371
#> Thu Sep 06 12:57:28 2018 .... Completed iteration: 5 | logLik: -1265977.42998371
#> Thu Sep 06 12:57:28 2018 .... Completed iteration: 6 | logLik: -1265977.81160925
#> Thu Sep 06 12:57:28 2018 .... Completed iteration: 7 | logLik: -1265977.42998371
#> Thu Sep 06 12:57:28 2018 .... Completed iteration: 8 | logLik: -1265977.42998371
#> Thu Sep 06 12:57:28 2018 .... Completed iteration: 9 | logLik: -1265977.42998371
#> Thu Sep 06 12:57:28 2018 .... Determining if any cell clusters should be split.
#> Thu Sep 06 12:57:28 2018 .... No additional splitting was performed.
#> Thu Sep 06 12:57:28 2018 .... Determining if any gene clusters should be split.
#> Thu Sep 06 12:57:28 2018 .... No additional splitting was performed.
#> Thu Sep 06 12:57:28 2018 .... Completed iteration: 10 | logLik: -1265977.42998371
#> Thu Sep 06 12:57:28 2018 .... Completed iteration: 11 | logLik: -1265977.81160925
#> Thu Sep 06 12:57:28 2018 .... Completed iteration: 12 | logLik: -1265977.81160925
#> Thu Sep 06 12:57:28 2018 .... Completed iteration: 13 | logLik: -1265977.81160925
#> Thu Sep 06 12:57:28 2018 .... Determining if any cell clusters should be split.
#> Thu Sep 06 12:57:28 2018 .... No additional splitting was performed.
#> Thu Sep 06 12:57:28 2018 .... Determining if any gene clusters should be split.
#> Thu Sep 06 12:57:29 2018 .... No additional splitting was performed.
#> Thu Sep 06 12:57:29 2018 .... Completed iteration: 14 | logLik: -1265977.81160925
#> Thu Sep 06 12:57:29 2018 .. Finished chain 3 with seed 12347
#> --------------------------------------------------------------------
#> Completed Celda_CG. Total time: 4.209606 secs
#> --------------------------------------------------------------------
celda.tsne <- celdaTsne(counts = sim.res$counts, celda.mod = celda_cg)
plotDimReduceCluster(dim1 = celda.tsne[,1], dim2 = celda.tsne[,2],cluster = as.factor(celda_cg$z),specific_clusters = c(1,2,3))