Create a scatterplot based off of a matrix containing the celda state probabilities per cell.

Create a scatterplot based off of a matrix containing the celda state probabilities per cell.

plotDimReduceState(dim1, dim2, counts, celda.mod, modules = NULL,
  rescale = TRUE, size = 1, xlab = "Dimension_1", ylab = "Dimension_2",
  color_low = "grey", color_mid = NULL, color_high = "blue")

Arguments

dim1	Numeric vector. First dimension from data dimensionality reduction output.
dim2	Numeric vector. Second dimension from data dimensionality reduction output.
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_G" or "celda_CG".
modules	Character vector. Module(s) from celda model to be plotted.
rescale	Logical. Whether rows of the matrix should be rescaled to [0,1]. Default TRUE.
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".
color_low	Character. A color available from `colors()`. The color will be used to signify the lowest values on the scale. Default 'grey'.
color_mid	Character. A color available from `colors()`. The color will be used to signify the midpoint on the scale.
color_high	Character. A color available from `colors()`. The color will be used to signify the highest values on the scale. Default 'blue'.

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 12:57:59 2018 .. Initializing chain 1 with 'random' (seed=12345)
#> Thu Sep 06 12:57:59 2018 .... Completed iteration: 1 | logLik: -1292432.99348905
#> Thu Sep 06 12:57:59 2018 .... Completed iteration: 2 | logLik: -1271152.8119707
#> Thu Sep 06 12:57:59 2018 .... Completed iteration: 3 | logLik: -1271146.08792976
#> Thu Sep 06 12:57:59 2018 .... Completed iteration: 4 | logLik: -1271142.13405322
#> Thu Sep 06 12:57:59 2018 .... Completed iteration: 5 | logLik: -1271138.7926281
#> Thu Sep 06 12:57:59 2018 .... Completed iteration: 6 | logLik: -1271139.37518801
#> Thu Sep 06 12:58:00 2018 .... Completed iteration: 7 | logLik: -1271135.02027059
#> Thu Sep 06 12:58:00 2018 .... Completed iteration: 8 | logLik: -1271133.69255723
#> Thu Sep 06 12:58:00 2018 .... Completed iteration: 9 | logLik: -1271131.24555386
#> Thu Sep 06 12:58:00 2018 .... Determining if any cell clusters should be split.
#> Thu Sep 06 12:58:00 2018 .... Cluster 1 was reassigned and cluster 3 was split in two.
#> Thu Sep 06 12:58:00 2018 .... Determining if any gene clusters should be split.
#> Thu Sep 06 12:58:00 2018 .... No additional splitting was performed.
#> Thu Sep 06 12:58:00 2018 .... Completed iteration: 10 | logLik: -1265977.81160925
#> Thu Sep 06 12:58:00 2018 .... Completed iteration: 11 | logLik: -1265977.81160925
#> Thu Sep 06 12:58:00 2018 .... Completed iteration: 12 | logLik: -1265977.42998371
#> Thu Sep 06 12:58:00 2018 .... Completed iteration: 13 | logLik: -1265977.81160925
#> Thu Sep 06 12:58:00 2018 .... Completed iteration: 14 | logLik: -1265977.42998371
#> Thu Sep 06 12:58:00 2018 .... Completed iteration: 15 | logLik: -1265977.42998371
#> Thu Sep 06 12:58:00 2018 .... Completed iteration: 16 | logLik: -1265977.42998371
#> Thu Sep 06 12:58:00 2018 .... Completed iteration: 17 | logLik: -1265977.81160925
#> Thu Sep 06 12:58:00 2018 .... Completed iteration: 18 | logLik: -1265977.42998371
#> Thu Sep 06 12:58:00 2018 .... Completed iteration: 19 | logLik: -1265977.42998371
#> Thu Sep 06 12:58:00 2018 .... Determining if any cell clusters should be split.
#> Thu Sep 06 12:58:01 2018 .... No additional splitting was performed.
#> Thu Sep 06 12:58:01 2018 .... Completed iteration: 20 | logLik: -1265977.42998371
#> Thu Sep 06 12:58:01 2018 .... Completed iteration: 21 | logLik: -1265977.81160925
#> Thu Sep 06 12:58:01 2018 .... Determining if any cell clusters should be split.
#> Thu Sep 06 12:58:01 2018 .... No additional splitting was performed.
#> Thu Sep 06 12:58:01 2018 .... Determining if any gene clusters should be split.
#> Thu Sep 06 12:58:01 2018 .... No additional splitting was performed.
#> Thu Sep 06 12:58:01 2018 .... Completed iteration: 22 | logLik: -1265977.81160925
#> Thu Sep 06 12:58:01 2018 .. Finished chain 1 with seed 12345
#> Thu Sep 06 12:58:01 2018 .. Initializing chain 2 with 'random' (seed=12346)
#> Thu Sep 06 12:58:01 2018 .... Completed iteration: 1 | logLik: -1296147.64459921
#> Thu Sep 06 12:58:01 2018 .... Completed iteration: 2 | logLik: -1273614.61367925
#> Thu Sep 06 12:58:01 2018 .... Completed iteration: 3 | logLik: -1271640.01823375
#> Thu Sep 06 12:58:01 2018 .... Completed iteration: 4 | logLik: -1271150.85741638
#> Thu Sep 06 12:58:01 2018 .... Completed iteration: 5 | logLik: -1270826.33540845
#> Thu Sep 06 12:58:01 2018 .... Completed iteration: 6 | logLik: -1268220.93677393
#> Thu Sep 06 12:58:01 2018 .... Completed iteration: 7 | logLik: -1265977.42998371
#> Thu Sep 06 12:58:01 2018 .... Completed iteration: 8 | logLik: -1265977.81160925
#> Thu Sep 06 12:58:01 2018 .... Completed iteration: 9 | logLik: -1265981.10028326
#> Thu Sep 06 12:58:01 2018 .... Determining if any cell clusters should be split.
#> Thu Sep 06 12:58:01 2018 .... No additional splitting was performed.
#> Thu Sep 06 12:58:01 2018 .... Determining if any gene clusters should be split.
#> Thu Sep 06 12:58:02 2018 .... No additional splitting was performed.
#> Thu Sep 06 12:58:02 2018 .... Completed iteration: 10 | logLik: -1265977.42998371
#> Thu Sep 06 12:58:02 2018 .... Completed iteration: 11 | logLik: -1265977.81160925
#> Thu Sep 06 12:58:02 2018 .... Completed iteration: 12 | logLik: -1265977.42998371
#> Thu Sep 06 12:58:02 2018 .... Completed iteration: 13 | logLik: -1265977.81160925
#> Thu Sep 06 12:58:02 2018 .... Completed iteration: 14 | logLik: -1265977.81160925
#> Thu Sep 06 12:58:02 2018 .... Completed iteration: 15 | logLik: -1265977.81160925
#> Thu Sep 06 12:58:02 2018 .... Completed iteration: 16 | logLik: -1265977.42998371
#> Thu Sep 06 12:58:02 2018 .... Determining if any cell clusters should be split.
#> Thu Sep 06 12:58:02 2018 .... No additional splitting was performed.
#> Thu Sep 06 12:58:02 2018 .... Determining if any gene clusters should be split.
#> Thu Sep 06 12:58:02 2018 .... No additional splitting was performed.
#> Thu Sep 06 12:58:02 2018 .... Completed iteration: 17 | logLik: -1265977.42998371
#> Thu Sep 06 12:58:02 2018 .. Finished chain 2 with seed 12346
#> Thu Sep 06 12:58:02 2018 .. Initializing chain 3 with 'random' (seed=12347)
#> Thu Sep 06 12:58:02 2018 .... Completed iteration: 1 | logLik: -1298276.1895605
#> Thu Sep 06 12:58:02 2018 .... Completed iteration: 2 | logLik: -1270053.97340606
#> Thu Sep 06 12:58:02 2018 .... Completed iteration: 3 | logLik: -1266751.51933782
#> Thu Sep 06 12:58:02 2018 .... Completed iteration: 4 | logLik: -1265977.42998371
#> Thu Sep 06 12:58:02 2018 .... Completed iteration: 5 | logLik: -1265977.42998371
#> Thu Sep 06 12:58:02 2018 .... Completed iteration: 6 | logLik: -1265977.81160925
#> Thu Sep 06 12:58:02 2018 .... Completed iteration: 7 | logLik: -1265977.42998371
#> Thu Sep 06 12:58:02 2018 .... Completed iteration: 8 | logLik: -1265977.42998371
#> Thu Sep 06 12:58:02 2018 .... Completed iteration: 9 | logLik: -1265977.42998371
#> Thu Sep 06 12:58:02 2018 .... Determining if any cell clusters should be split.
#> Thu Sep 06 12:58:02 2018 .... No additional splitting was performed.
#> Thu Sep 06 12:58:02 2018 .... Determining if any gene clusters should be split.
#> Thu Sep 06 12:58:03 2018 .... No additional splitting was performed.
#> Thu Sep 06 12:58:03 2018 .... Completed iteration: 10 | logLik: -1265977.42998371
#> Thu Sep 06 12:58:03 2018 .... Completed iteration: 11 | logLik: -1265977.81160925
#> Thu Sep 06 12:58:03 2018 .... Completed iteration: 12 | logLik: -1265977.81160925
#> Thu Sep 06 12:58:03 2018 .... Completed iteration: 13 | logLik: -1265977.81160925
#> Thu Sep 06 12:58:03 2018 .... Determining if any cell clusters should be split.
#> Thu Sep 06 12:58:03 2018 .... No additional splitting was performed.
#> Thu Sep 06 12:58:03 2018 .... Determining if any gene clusters should be split.
#> Thu Sep 06 12:58:03 2018 .... No additional splitting was performed.
#> Thu Sep 06 12:58:03 2018 .... Completed iteration: 14 | logLik: -1265977.81160925
#> Thu Sep 06 12:58:03 2018 .. Finished chain 3 with seed 12347
#> --------------------------------------------------------------------
#> Completed Celda_CG. Total time: 3.8418 secs
#> --------------------------------------------------------------------
celda.tsne <- celdaTsne(counts = sim.res$counts, celda.mod = celda_cg)
plotDimReduceState(dim1 = celda.tsne[,1], dim2 = celda.tsne[,2],
                   counts = sim.res$counts, celda.mod = celda_cg, modules = c("L1","L2"))