diff --git a/DESCRIPTION b/DESCRIPTION index a878ea7b..7f4a6c93 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: celda Title: CEllular Latent Dirichlet Allocation -Version: 1.9.2 +Version: 1.9.3 Authors@R: c(person("Joshua", "Campbell", email = "camp@bu.edu", role = c("aut", "cre")), person("Shiyi", "Yang", email="syyang@bu.edu", role = c("aut")), diff --git a/NEWS.md b/NEWS.md index 2bc719ae..ca479093 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,6 +1,9 @@ +# celda v1.9.3 (2021-10-04) + * Fixed bug in checking background matrix with decontX * Switched to using Github Actions for Continuous Integration * Fixed plotting bugs in celda results reports +* Speed up final step in decontX when creating final decontaminated matrix # celda v1.9.2 (2021-07-19) diff --git a/_pkgdown.yml b/_pkgdown.yml index a2dbb58b..d779a342 100755 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -34,6 +34,7 @@ reference: - plotDecontXContamination - plotDecontXMarkerExpression - plotDecontXMarkerPercentage + - decontXcounts - title: Functions for determining the numbers of clusters in celda @@ -101,7 +102,7 @@ navbar: title: "celda" left: - icon: fa-home fa-lg - href: http://celda.camplab.net/ + href: https://www.camplab.net/celda - text: "Installation" href: articles/articles/installation.html - text: "Vignettes" diff --git a/docs/404.html b/docs/404.html index 7f5f367d..764c403b 100644 --- a/docs/404.html +++ b/docs/404.html @@ -71,14 +71,14 @@ celda - 1.9.2 + 1.9.3 -
+
+

+celda v1.9.3 (2021-10-04)

+ +
+

-celda 1.9.2

+celda v1.9.2 (2021-07-19) +
+
+

+celda v1.7.7 (2021-04-12):

+ +
+
+

+celda v1.7.6 (2021-04-04):

+ +
+
+

+celda v1.7.4 (2021-03-09):

+ +
+
+

+celda v1.1.6 (2019-07-16):

+ +
+
+

+celda v1.1.4 (2019-05-28):

+ +
+
+

+celda v1.1.3 (2019-05-14):

+ +
+
+

+celda v1.1.2 (2019-05-14):

+ +
+
+

+celda v1.0.1 (2019-05-09):

+ +
+
+

+celda v0.99.34 (2019-04-23):

+ +
+
+

+celda v0.99.23 (2019-04-10):

+ +
+
+

+celda v0.99.22 (2019-04-09):

+ +
+
+

+celda v0.99.8 (2019-03-11):

+ +
+
+

+celda v0.99.0 (2018-05-15):

+
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 726247bb..8e3bb132 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -7,5 +7,5 @@ articles: articles/installation: installation.html celda: celda.html decontX: decontX.html -last_built: 2021-09-29T16:24Z +last_built: 2021-10-04T16:07Z diff --git a/docs/reference/appendCeldaList.html b/docs/reference/appendCeldaList.html index 9a5295ab..e8e38f57 100644 --- a/docs/reference/appendCeldaList.html +++ b/docs/reference/appendCeldaList.html @@ -73,14 +73,14 @@ celda - 1.9.2 + 1.9.3
#> --------------------------------------------------
#> Starting Celda_C: Clustering cells.
#> --------------------------------------------------
#> Wed Sep 29 12:24:45 2021 .. Initializing 'z' in chain 1 with 'split'
#> Wed Sep 29 12:24:45 2021 .... Completed iteration: 1 | logLik: -1282027.27277705
#> Wed Sep 29 12:24:45 2021 .... Completed iteration: 2 | logLik: -1282027.27277705
#> Wed Sep 29 12:24:45 2021 .. Finished chain 1
#> --------------------------------------------------
#> Completed Celda_C. Total time: 0.1618769 secs
#> --------------------------------------------------
+
#> --------------------------------------------------
#> Starting Celda_C: Clustering cells.
#> --------------------------------------------------
#> Mon Oct 4 12:07:37 2021 .. Initializing 'z' in chain 1 with 'split'
#> Mon Oct 4 12:07:37 2021 .... Completed iteration: 1 | logLik: -1282027.27277705
#> Mon Oct 4 12:07:37 2021 .... Completed iteration: 2 | logLik: -1282027.27277705
#> Mon Oct 4 12:07:37 2021 .. Finished chain 1
#> --------------------------------------------------
#> Completed Celda_C. Total time: 0.137078 secs
#> --------------------------------------------------
#> --------------------------------------------------
#> Starting Celda_CG: Clustering cells and genes.
#> --------------------------------------------------
#> Wed Sep 29 12:24:46 2021 .. Initializing 'z' in chain 1 with 'split'
#> Wed Sep 29 12:24:46 2021 .. Initializing 'y' in chain 1 with 'split'
#> Wed Sep 29 12:24:49 2021 .... Completed iteration: 1 | logLik: -1215542.98684529
#> Wed Sep 29 12:24:49 2021 .... Completed iteration: 2 | logLik: -1215541.0958389
#> Wed Sep 29 12:24:49 2021 .... Completed iteration: 3 | logLik: -1215541.0958389
#> Wed Sep 29 12:24:49 2021 .... Completed iteration: 4 | logLik: -1215542.98684529
#> Wed Sep 29 12:24:49 2021 .... Completed iteration: 5 | logLik: -1215541.0958389
#> Wed Sep 29 12:24:50 2021 .... Completed iteration: 6 | logLik: -1215541.0958389
#> Wed Sep 29 12:24:50 2021 .... Completed iteration: 7 | logLik: -1215541.0958389
#> Wed Sep 29 12:24:50 2021 .... Completed iteration: 8 | logLik: -1215541.0958389
#> Wed Sep 29 12:24:50 2021 .... Completed iteration: 9 | logLik: -1215541.0958389
#> Wed Sep 29 12:24:50 2021 .... Determining if any gene clusters should be split.
#> Wed Sep 29 12:24:50 2021 .... No additional splitting was performed.
#> Wed Sep 29 12:24:50 2021 .... Determining if any cell clusters should be split.
#> Wed Sep 29 12:24:50 2021 .... No additional splitting was performed.
#> Wed Sep 29 12:24:50 2021 .... Completed iteration: 10 | logLik: -1215541.0958389
#> Wed Sep 29 12:24:50 2021 .... Determining if any cell clusters should be split.
#> Wed Sep 29 12:24:50 2021 .... No additional splitting was performed.
#> Wed Sep 29 12:24:50 2021 .... Completed iteration: 11 | logLik: -1215541.0958389
#> Wed Sep 29 12:24:50 2021 .. Finished chain 1
#> --------------------------------------------------
#> Completed Celda_CG. Total time: 4.13753 secs
#> --------------------------------------------------
+
#> --------------------------------------------------
#> Starting Celda_CG: Clustering cells and genes.
#> --------------------------------------------------
#> Mon Oct 4 12:07:38 2021 .. Initializing 'z' in chain 1 with 'split'
#> Mon Oct 4 12:07:38 2021 .. Initializing 'y' in chain 1 with 'split'
#> Mon Oct 4 12:07:41 2021 .... Completed iteration: 1 | logLik: -1215542.98684529
#> Mon Oct 4 12:07:41 2021 .... Completed iteration: 2 | logLik: -1215541.0958389
#> Mon Oct 4 12:07:41 2021 .... Completed iteration: 3 | logLik: -1215541.0958389
#> Mon Oct 4 12:07:41 2021 .... Completed iteration: 4 | logLik: -1215542.98684529
#> Mon Oct 4 12:07:41 2021 .... Completed iteration: 5 | logLik: -1215541.0958389
#> Mon Oct 4 12:07:41 2021 .... Completed iteration: 6 | logLik: -1215541.0958389
#> Mon Oct 4 12:07:41 2021 .... Completed iteration: 7 | logLik: -1215541.0958389
#> Mon Oct 4 12:07:41 2021 .... Completed iteration: 8 | logLik: -1215541.0958389
#> Mon Oct 4 12:07:41 2021 .... Completed iteration: 9 | logLik: -1215541.0958389
#> Mon Oct 4 12:07:41 2021 .... Determining if any gene clusters should be split.
#> Mon Oct 4 12:07:41 2021 .... No additional splitting was performed.
#> Mon Oct 4 12:07:41 2021 .... Determining if any cell clusters should be split.
#> Mon Oct 4 12:07:41 2021 .... No additional splitting was performed.
#> Mon Oct 4 12:07:41 2021 .... Completed iteration: 10 | logLik: -1215541.0958389
#> Mon Oct 4 12:07:41 2021 .... Determining if any cell clusters should be split.
#> Mon Oct 4 12:07:41 2021 .... No additional splitting was performed.
#> Mon Oct 4 12:07:41 2021 .... Completed iteration: 11 | logLik: -1215541.0958389
#> Mon Oct 4 12:07:41 2021 .. Finished chain 1
#> --------------------------------------------------
#> Completed Celda_CG. Total time: 3.250677 secs
#> --------------------------------------------------
#> --------------------------------------------------
#> Starting Celda_G: Clustering genes.
#> --------------------------------------------------
#> Mon Oct 4 12:07:41 2021 .. Initializing 'y' in chain 1 with 'split'
#> Mon Oct 4 12:07:43 2021 .... Completed iteration: 1 | logLik: -290669.046132139
#> Mon Oct 4 12:07:43 2021 .... Completed iteration: 2 | logLik: -290669.046132139
#> Mon Oct 4 12:07:43 2021 .... Completed iteration: 3 | logLik: -290669.046132139
#> Mon Oct 4 12:07:43 2021 .... Completed iteration: 4 | logLik: -290669.046132139
#> Mon Oct 4 12:07:43 2021 .... Completed iteration: 5 | logLik: -290669.046132139
#> Mon Oct 4 12:07:43 2021 .... Completed iteration: 6 | logLik: -290669.046132139
#> Mon Oct 4 12:07:43 2021 .... Completed iteration: 7 | logLik: -290669.046132139
#> Mon Oct 4 12:07:44 2021 .... Completed iteration: 8 | logLik: -290669.046132139
#> Mon Oct 4 12:07:44 2021 .... Completed iteration: 9 | logLik: -290669.046132139
#> Mon Oct 4 12:07:44 2021 .... Determining if any gene clusters should be split.
#> Mon Oct 4 12:07:44 2021 .... No additional splitting was performed.
#> Mon Oct 4 12:07:44 2021 .... Completed iteration: 10 | logLik: -290669.046132139
#> Mon Oct 4 12:07:44 2021 .... Completed iteration: 11 | logLik: -290669.046132139
#> Mon Oct 4 12:07:44 2021 .. Finished chain 1
#> --------------------------------------------------
#> Completed Celda_G. Total time: 2.44341 secs
#> --------------------------------------------------
sce <- SingleCellExperiment(list(counts = s$observedCounts)) sce <- decontX(sce) -
#> --------------------------------------------------
#> Starting DecontX
#> --------------------------------------------------
#> Wed Sep 29 12:24:56 2021 .. Analyzing all cells
#> Wed Sep 29 12:24:56 2021 .... Converting to sparse matrix
#> Wed Sep 29 12:24:57 2021 .... Generating UMAP and estimating cell types
#> Wed Sep 29 12:25:00 2021 .... Estimating contamination
#> Wed Sep 29 12:25:00 2021 ...... Completed iteration: 9 | converge: 0.0009154
#> --------------------------------------------------
#> Completed DecontX. Total time: 3.44309 secs
#> --------------------------------------------------
+
#> --------------------------------------------------
#> Starting DecontX
#> --------------------------------------------------
#> Mon Oct 4 12:07:46 2021 .. Analyzing all cells
#> Mon Oct 4 12:07:46 2021 .... Converting to sparse matrix
#> Mon Oct 4 12:07:46 2021 .... Generating UMAP and estimating cell types
#> Mon Oct 4 12:07:49 2021 .... Estimating contamination
#> Mon Oct 4 12:07:49 2021 ...... Completed iteration: 9 | converge: 0.0009154
#> Mon Oct 4 12:07:49 2021 .. Calculating final decontaminated matrix
#> --------------------------------------------------
#> Completed DecontX. Total time: 2.786641 secs
#> --------------------------------------------------
# Plot contamination on UMAP plotDecontXContamination(sce)
diff --git a/docs/reference/decontXcounts.html b/docs/reference/decontXcounts.html index 6bdec5d7..01eb9624 100644 --- a/docs/reference/decontXcounts.html +++ b/docs/reference/decontXcounts.html @@ -73,14 +73,14 @@ celda - 1.9.2 + 1.9.3
#> ==================================================
#> Starting recursive cell population splitting.
#> ==================================================
#> Wed Sep 29 12:26:23 2021 .. Initializing with 3 populations
#> Wed Sep 29 12:26:23 2021 .. Current cell population 4 | logLik: -1225755.01101897
#> Wed Sep 29 12:26:23 2021 .. Current cell population 5 | logLik: -1213677.60126784
#> Wed Sep 29 12:26:23 2021 .. Current cell population 6 | logLik: -1213903.59449854
#> Wed Sep 29 12:26:23 2021 .. Current cell population 7 | logLik: -1214081.54311397
#> Wed Sep 29 12:26:23 2021 .. Calculating perplexity
#> ==================================================
#> Completed recursive cell population splitting. Total time: 0.49826 secs
#> ==================================================
+
#> ==================================================
#> Starting recursive cell population splitting.
#> ==================================================
#> Mon Oct 4 12:08:56 2021 .. Initializing with 3 populations
#> Mon Oct 4 12:08:56 2021 .. Current cell population 4 | logLik: -1225755.01101897
#> Mon Oct 4 12:08:56 2021 .. Current cell population 5 | logLik: -1213677.60126784
#> Mon Oct 4 12:08:56 2021 .. Current cell population 6 | logLik: -1213903.59449854
#> Mon Oct 4 12:08:56 2021 .. Current cell population 7 | logLik: -1214081.54311397
#> Mon Oct 4 12:08:56 2021 .. Calculating perplexity
#> ==================================================
#> Completed recursive cell population splitting. Total time: 0.3744612 secs
#> ==================================================
## Alternatively, first identify features modules using ## \link{recursiveSplitModule} moduleSplit <- recursiveSplitModule(sceCeldaCG, initialL = 3, maxL = 15) -
#> ==================================================
#> Starting recursive module splitting.
#> ==================================================
#> Wed Sep 29 12:26:24 2021 .. Collapsing to 100 temporary cell populations
#> Wed Sep 29 12:26:25 2021 .. Initializing with 3 modules
#> Wed Sep 29 12:26:25 2021 .. Created module 4 | logLik: -1241379.90928455
#> Wed Sep 29 12:26:25 2021 .. Created module 5 | logLik: -1235212.7977535
#> Wed Sep 29 12:26:25 2021 .. Created module 6 | logLik: -1232789.9817561
#> Wed Sep 29 12:26:25 2021 .. Created module 7 | logLik: -1227246.66090571
#> Wed Sep 29 12:26:25 2021 .. Created module 8 | logLik: -1223898.757694
#> Wed Sep 29 12:26:26 2021 .. Created module 9 | logLik: -1221848.26936098
#> Wed Sep 29 12:26:26 2021 .. Created module 10 | logLik: -1220147.96681948
#> Wed Sep 29 12:26:26 2021 .. Created module 11 | logLik: -1220818.37022325
#> Wed Sep 29 12:26:26 2021 .. Created module 12 | logLik: -1221489.07685946
#> Wed Sep 29 12:26:26 2021 .. Created module 13 | logLik: -1222032.53497571
#> Wed Sep 29 12:26:26 2021 .. Created module 14 | logLik: -1222712.17543857
#> Wed Sep 29 12:26:26 2021 .. Created module 15 | logLik: -1223268.97596756
#> Wed Sep 29 12:26:26 2021 .. Calculating perplexity
#> ==================================================
#> Completed recursive module splitting. Total time: 2.821409 secs
#> ==================================================
plotGridSearchPerplexity(moduleSplit) +
#> ==================================================
#> Starting recursive module splitting.
#> ==================================================
#> Mon Oct 4 12:08:56 2021 .. Collapsing to 100 temporary cell populations
#> Mon Oct 4 12:08:57 2021 .. Initializing with 3 modules
#> Mon Oct 4 12:08:57 2021 .. Created module 4 | logLik: -1241379.90928455
#> Mon Oct 4 12:08:57 2021 .. Created module 5 | logLik: -1235212.7977535
#> Mon Oct 4 12:08:58 2021 .. Created module 6 | logLik: -1232789.9817561
#> Mon Oct 4 12:08:58 2021 .. Created module 7 | logLik: -1227246.66090571
#> Mon Oct 4 12:08:58 2021 .. Created module 8 | logLik: -1223898.757694
#> Mon Oct 4 12:08:58 2021 .. Created module 9 | logLik: -1221848.26936098
#> Mon Oct 4 12:08:58 2021 .. Created module 10 | logLik: -1220147.96681948
#> Mon Oct 4 12:08:58 2021 .. Created module 11 | logLik: -1220818.37022325
#> Mon Oct 4 12:08:58 2021 .. Created module 12 | logLik: -1221489.07685946
#> Mon Oct 4 12:08:58 2021 .. Created module 13 | logLik: -1222032.53497571
#> Mon Oct 4 12:08:58 2021 .. Created module 14 | logLik: -1222712.17543857
#> Mon Oct 4 12:08:58 2021 .. Created module 15 | logLik: -1223268.97596756
#> Mon Oct 4 12:08:58 2021 .. Calculating perplexity
#> ==================================================
#> Completed recursive module splitting. Total time: 2.250609 secs
#> ==================================================
plotGridSearchPerplexity(moduleSplit)
moduleSplitSelect <- subsetCeldaList(moduleSplit, list(L = 10)) ## Then use module labels for initialization in \link{recursiveSplitCell} to ## produce \link{celda_CG} bi-clustering models cellSplit <- recursiveSplitCell(sceCeldaCG, initialK = 3, maxK = 7, yInit = celdaModules(moduleSplitSelect)) -
#> ==================================================
#> Starting recursive cell population splitting.
#> ==================================================
#> Wed Sep 29 12:26:27 2021 .. Collapsing to 10 modules
#> Wed Sep 29 12:26:27 2021 .. Initializing with 3 populations
#> Wed Sep 29 12:26:28 2021 .. Current cell population 4 | logLik: -1225286.49558716
#> Wed Sep 29 12:26:28 2021 .. Current cell population 5 | logLik: -1212955.15575681
#> Wed Sep 29 12:26:28 2021 .. Current cell population 6 | logLik: -1212982.74290613
#> Wed Sep 29 12:26:28 2021 .. Current cell population 7 | logLik: -1213005.40337891
#> Wed Sep 29 12:26:28 2021 .. Calculating perplexity
#> ==================================================
#> Completed recursive cell population splitting. Total time: 1.327111 secs
#> ==================================================
plotGridSearchPerplexity(cellSplit) +
#> ==================================================
#> Starting recursive cell population splitting.
#> ==================================================
#> Mon Oct 4 12:08:59 2021 .. Collapsing to 10 modules
#> Mon Oct 4 12:08:59 2021 .. Initializing with 3 populations
#> Mon Oct 4 12:09:00 2021 .. Current cell population 4 | logLik: -1225286.49558716
#> Mon Oct 4 12:09:00 2021 .. Current cell population 5 | logLik: -1212955.15575681
#> Mon Oct 4 12:09:00 2021 .. Current cell population 6 | logLik: -1212982.74290613
#> Mon Oct 4 12:09:00 2021 .. Current cell population 7 | logLik: -1213005.40337891
#> Mon Oct 4 12:09:00 2021 .. Calculating perplexity
#> ==================================================
#> Completed recursive cell population splitting. Total time: 1.471492 secs
#> ==================================================
plotGridSearchPerplexity(cellSplit)
sce <- subsetCeldaList(cellSplit, list(K = 5, L = 10)) data(celdaCGSim, celdaCSim) ## Create models that range from K = 3 to K = 7 by recursively splitting ## cell populations into two to produce \link{celda_C} cell clustering models sce <- recursiveSplitCell(celdaCSim$counts, initialK = 3, maxK = 7) -
#> ==================================================
#> Starting recursive cell population splitting.
#> ==================================================
#> Wed Sep 29 12:26:29 2021 .. Initializing with 3 populations
#> Wed Sep 29 12:26:29 2021 .. Current cell population 4 | logLik: -1341630.1679001
#> Wed Sep 29 12:26:29 2021 .. Current cell population 5 | logLik: -1327506.91718317
#> Wed Sep 29 12:26:29 2021 .. Current cell population 6 | logLik: -1315227.54586167
#> Wed Sep 29 12:26:29 2021 .. Current cell population 7 | logLik: -1304393.65802293
#> Wed Sep 29 12:26:29 2021 .. Calculating perplexity
#> ==================================================
#> Completed recursive cell population splitting. Total time: 0.4102552 secs
#> ==================================================
+
#> ==================================================
#> Starting recursive cell population splitting.
#> ==================================================
#> Mon Oct 4 12:09:01 2021 .. Initializing with 3 populations
#> Mon Oct 4 12:09:01 2021 .. Current cell population 4 | logLik: -1341630.1679001
#> Mon Oct 4 12:09:01 2021 .. Current cell population 5 | logLik: -1327506.91718317
#> Mon Oct 4 12:09:01 2021 .. Current cell population 6 | logLik: -1315227.54586167
#> Mon Oct 4 12:09:01 2021 .. Current cell population 7 | logLik: -1304393.65802293
#> Mon Oct 4 12:09:01 2021 .. Calculating perplexity
#> ==================================================
#> Completed recursive cell population splitting. Total time: 0.3327959 secs
#> ==================================================
## Alternatively, first identify features modules using ## \link{recursiveSplitModule} moduleSplit <- recursiveSplitModule(celdaCGSim$counts, initialL = 3, maxL = 15) -
#> ==================================================
#> Starting recursive module splitting.
#> ==================================================
#> Wed Sep 29 12:26:29 2021 .. Collapsing to 100 temporary cell populations
#> Wed Sep 29 12:26:30 2021 .. Initializing with 3 modules
#> Wed Sep 29 12:26:31 2021 .. Created module 4 | logLik: -1243396.62348886
#> Wed Sep 29 12:26:31 2021 .. Created module 5 | logLik: -1237610.11790137
#> Wed Sep 29 12:26:31 2021 .. Created module 6 | logLik: -1232128.87013396
#> Wed Sep 29 12:26:31 2021 .. Created module 7 | logLik: -1227611.8250329
#> Wed Sep 29 12:26:31 2021 .. Created module 8 | logLik: -1225618.06184004
#> Wed Sep 29 12:26:31 2021 .. Created module 9 | logLik: -1223967.77531912
#> Wed Sep 29 12:26:31 2021 .. Created module 10 | logLik: -1222801.11395987
#> Wed Sep 29 12:26:31 2021 .. Created module 11 | logLik: -1223402.66903597
#> Wed Sep 29 12:26:31 2021 .. Created module 12 | logLik: -1224026.19892208
#> Wed Sep 29 12:26:31 2021 .. Created module 13 | logLik: -1224675.63005464
#> Wed Sep 29 12:26:32 2021 .. Created module 14 | logLik: -1225317.91966369
#> Wed Sep 29 12:26:32 2021 .. Created module 15 | logLik: -1225971.50555157
#> Wed Sep 29 12:26:32 2021 .. Calculating perplexity
#> ==================================================
#> Completed recursive module splitting. Total time: 3.130327 secs
#> ==================================================
plotGridSearchPerplexity(moduleSplit) +
#> ==================================================
#> Starting recursive module splitting.
#> ==================================================
#> Mon Oct 4 12:09:01 2021 .. Collapsing to 100 temporary cell populations
#> Mon Oct 4 12:09:02 2021 .. Initializing with 3 modules
#> Mon Oct 4 12:09:02 2021 .. Created module 4 | logLik: -1243396.62348886
#> Mon Oct 4 12:09:02 2021 .. Created module 5 | logLik: -1237610.11790137
#> Mon Oct 4 12:09:02 2021 .. Created module 6 | logLik: -1232128.87013396
#> Mon Oct 4 12:09:02 2021 .. Created module 7 | logLik: -1227611.8250329
#> Mon Oct 4 12:09:02 2021 .. Created module 8 | logLik: -1225618.06184004
#> Mon Oct 4 12:09:02 2021 .. Created module 9 | logLik: -1223967.77531912
#> Mon Oct 4 12:09:02 2021 .. Created module 10 | logLik: -1222801.11395987
#> Mon Oct 4 12:09:03 2021 .. Created module 11 | logLik: -1223402.66903597
#> Mon Oct 4 12:09:03 2021 .. Created module 12 | logLik: -1224026.19892208
#> Mon Oct 4 12:09:03 2021 .. Created module 13 | logLik: -1224675.63005464
#> Mon Oct 4 12:09:03 2021 .. Created module 14 | logLik: -1225317.91966369
#> Mon Oct 4 12:09:03 2021 .. Created module 15 | logLik: -1225971.50555157
#> Mon Oct 4 12:09:03 2021 .. Calculating perplexity
#> ==================================================
#> Completed recursive module splitting. Total time: 2.125219 secs
#> ==================================================
plotGridSearchPerplexity(moduleSplit)
moduleSplitSelect <- subsetCeldaList(moduleSplit, list(L = 10)) ## Then use module labels for initialization in \link{recursiveSplitCell} to ## produce \link{celda_CG} bi-clustering models cellSplit <- recursiveSplitCell(celdaCGSim$counts, initialK = 3, maxK = 7, yInit = celdaModules(moduleSplitSelect)) -
#> ==================================================
#> Starting recursive cell population splitting.
#> ==================================================
#> Wed Sep 29 12:26:33 2021 .. Collapsing to 10 modules
#> Wed Sep 29 12:26:33 2021 .. Initializing with 3 populations
#> Wed Sep 29 12:26:35 2021 .. Current cell population 4 | logLik: -1227944.5458832
#> Wed Sep 29 12:26:35 2021 .. Current cell population 5 | logLik: -1215605.08613503
#> Wed Sep 29 12:26:35 2021 .. Current cell population 6 | logLik: -1215627.62281773
#> Wed Sep 29 12:26:35 2021 .. Current cell population 7 | logLik: -1215651.32538066
#> Wed Sep 29 12:26:35 2021 .. Calculating perplexity
#> ==================================================
#> Completed recursive cell population splitting. Total time: 2.154625 secs
#> ==================================================
plotGridSearchPerplexity(cellSplit) +
#> ==================================================
#> Starting recursive cell population splitting.
#> ==================================================
#> Mon Oct 4 12:09:04 2021 .. Collapsing to 10 modules
#> Mon Oct 4 12:09:04 2021 .. Initializing with 3 populations
#> Mon Oct 4 12:09:05 2021 .. Current cell population 4 | logLik: -1227944.5458832
#> Mon Oct 4 12:09:05 2021 .. Current cell population 5 | logLik: -1215605.08613503
#> Mon Oct 4 12:09:05 2021 .. Current cell population 6 | logLik: -1215627.62281773
#> Mon Oct 4 12:09:05 2021 .. Current cell population 7 | logLik: -1215651.32538066
#> Mon Oct 4 12:09:05 2021 .. Calculating perplexity
#> ==================================================
#> Completed recursive cell population splitting. Total time: 2.134903 secs
#> ==================================================
plotGridSearchPerplexity(cellSplit)
sce <- subsetCeldaList(cellSplit, list(K = 5, L = 10))
diff --git a/docs/reference/recursiveSplitModule.html b/docs/reference/recursiveSplitModule.html index 9a993138..65511b13 100644 --- a/docs/reference/recursiveSplitModule.html +++ b/docs/reference/recursiveSplitModule.html @@ -77,14 +77,14 @@ celda - 1.9.2 + 1.9.3
#> ==================================================
#> Starting recursive module splitting.
#> ==================================================
#> Wed Sep 29 12:26:36 2021 .. Collapsing to 100 temporary cell populations
#> Wed Sep 29 12:26:38 2021 .. Initializing with 3 modules
#> Wed Sep 29 12:26:38 2021 .. Created module 4 | logLik: -1241379.90928455
#> Wed Sep 29 12:26:38 2021 .. Created module 5 | logLik: -1235212.7977535
#> Wed Sep 29 12:26:38 2021 .. Created module 6 | logLik: -1232789.9817561
#> Wed Sep 29 12:26:38 2021 .. Created module 7 | logLik: -1227246.66090571
#> Wed Sep 29 12:26:38 2021 .. Created module 8 | logLik: -1223898.757694
#> Wed Sep 29 12:26:38 2021 .. Created module 9 | logLik: -1221848.26936098
#> Wed Sep 29 12:26:38 2021 .. Created module 10 | logLik: -1220147.96681948
#> Wed Sep 29 12:26:38 2021 .. Created module 11 | logLik: -1220818.37022325
#> Wed Sep 29 12:26:39 2021 .. Created module 12 | logLik: -1221489.07685946
#> Wed Sep 29 12:26:39 2021 .. Created module 13 | logLik: -1222032.53497571
#> Wed Sep 29 12:26:39 2021 .. Created module 14 | logLik: -1222712.17543857
#> Wed Sep 29 12:26:39 2021 .. Created module 15 | logLik: -1223268.97596756
#> Wed Sep 29 12:26:39 2021 .. Created module 16 | logLik: -1223841.4834406
#> Wed Sep 29 12:26:39 2021 .. Created module 17 | logLik: -1224394.02513994
#> Wed Sep 29 12:26:39 2021 .. Created module 18 | logLik: -1224863.41435811
#> Wed Sep 29 12:26:39 2021 .. Created module 19 | logLik: -1225480.30453125
#> Wed Sep 29 12:26:39 2021 .. Created module 20 | logLik: -1226156.47078695
#> Wed Sep 29 12:26:39 2021 .. Calculating perplexity
#> ==================================================
#> Completed recursive module splitting. Total time: 3.367581 secs
#> ==================================================
+
#> ==================================================
#> Starting recursive module splitting.
#> ==================================================
#> Mon Oct 4 12:09:07 2021 .. Collapsing to 100 temporary cell populations
#> Mon Oct 4 12:09:08 2021 .. Initializing with 3 modules
#> Mon Oct 4 12:09:08 2021 .. Created module 4 | logLik: -1241379.90928455
#> Mon Oct 4 12:09:08 2021 .. Created module 5 | logLik: -1235212.7977535
#> Mon Oct 4 12:09:08 2021 .. Created module 6 | logLik: -1232789.9817561
#> Mon Oct 4 12:09:08 2021 .. Created module 7 | logLik: -1227246.66090571
#> Mon Oct 4 12:09:08 2021 .. Created module 8 | logLik: -1223898.757694
#> Mon Oct 4 12:09:08 2021 .. Created module 9 | logLik: -1221848.26936098
#> Mon Oct 4 12:09:08 2021 .. Created module 10 | logLik: -1220147.96681948
#> Mon Oct 4 12:09:08 2021 .. Created module 11 | logLik: -1220818.37022325
#> Mon Oct 4 12:09:08 2021 .. Created module 12 | logLik: -1221489.07685946
#> Mon Oct 4 12:09:08 2021 .. Created module 13 | logLik: -1222032.53497571
#> Mon Oct 4 12:09:09 2021 .. Created module 14 | logLik: -1222712.17543857
#> Mon Oct 4 12:09:09 2021 .. Created module 15 | logLik: -1223268.97596756
#> Mon Oct 4 12:09:09 2021 .. Created module 16 | logLik: -1223841.4834406
#> Mon Oct 4 12:09:09 2021 .. Created module 17 | logLik: -1224394.02513994
#> Mon Oct 4 12:09:09 2021 .. Created module 18 | logLik: -1224863.41435811
#> Mon Oct 4 12:09:09 2021 .. Created module 19 | logLik: -1225480.30453125
#> Mon Oct 4 12:09:09 2021 .. Created module 20 | logLik: -1226156.47078695
#> Mon Oct 4 12:09:09 2021 .. Calculating perplexity
#> ==================================================
#> Completed recursive module splitting. Total time: 2.715739 secs
#> ==================================================
## Example results with perplexity plotGridSearchPerplexity(moduleSplit)
@@ -353,7 +353,7 @@

Examp ## into two moduleSplit <- recursiveSplitModule(celdaCGSim$counts, initialL = 3, maxL = 20) -

#> ==================================================
#> Starting recursive module splitting.
#> ==================================================
#> Wed Sep 29 12:26:40 2021 .. Collapsing to 100 temporary cell populations
#> Wed Sep 29 12:26:41 2021 .. Initializing with 3 modules
#> Wed Sep 29 12:26:42 2021 .. Created module 4 | logLik: -1243396.62348886
#> Wed Sep 29 12:26:42 2021 .. Created module 5 | logLik: -1237610.11790137
#> Wed Sep 29 12:26:42 2021 .. Created module 6 | logLik: -1232128.87013396
#> Wed Sep 29 12:26:42 2021 .. Created module 7 | logLik: -1227611.8250329
#> Wed Sep 29 12:26:42 2021 .. Created module 8 | logLik: -1225618.06184004
#> Wed Sep 29 12:26:42 2021 .. Created module 9 | logLik: -1223967.77531912
#> Wed Sep 29 12:26:42 2021 .. Created module 10 | logLik: -1222801.11395987
#> Wed Sep 29 12:26:42 2021 .. Created module 11 | logLik: -1223402.66903597
#> Wed Sep 29 12:26:42 2021 .. Created module 12 | logLik: -1224026.19892208
#> Wed Sep 29 12:26:42 2021 .. Created module 13 | logLik: -1224675.63005464
#> Wed Sep 29 12:26:42 2021 .. Created module 14 | logLik: -1225317.91966369
#> Wed Sep 29 12:26:43 2021 .. Created module 15 | logLik: -1225971.50555157
#> Wed Sep 29 12:26:43 2021 .. Created module 16 | logLik: -1226557.7881506
#> Wed Sep 29 12:26:43 2021 .. Created module 17 | logLik: -1227080.13473523
#> Wed Sep 29 12:26:43 2021 .. Created module 18 | logLik: -1227603.99622355
#> Wed Sep 29 12:26:43 2021 .. Created module 19 | logLik: -1228247.84169741
#> Wed Sep 29 12:26:43 2021 .. Created module 20 | logLik: -1228828.70617002
#> Wed Sep 29 12:26:43 2021 .. Calculating perplexity
#> ==================================================
#> Completed recursive module splitting. Total time: 3.758779 secs
#> ==================================================
+
#> ==================================================
#> Starting recursive module splitting.
#> ==================================================
#> Mon Oct 4 12:09:10 2021 .. Collapsing to 100 temporary cell populations
#> Mon Oct 4 12:09:11 2021 .. Initializing with 3 modules
#> Mon Oct 4 12:09:11 2021 .. Created module 4 | logLik: -1243396.62348886
#> Mon Oct 4 12:09:11 2021 .. Created module 5 | logLik: -1237610.11790137
#> Mon Oct 4 12:09:11 2021 .. Created module 6 | logLik: -1232128.87013396
#> Mon Oct 4 12:09:11 2021 .. Created module 7 | logLik: -1227611.8250329
#> Mon Oct 4 12:09:11 2021 .. Created module 8 | logLik: -1225618.06184004
#> Mon Oct 4 12:09:11 2021 .. Created module 9 | logLik: -1223967.77531912
#> Mon Oct 4 12:09:11 2021 .. Created module 10 | logLik: -1222801.11395987
#> Mon Oct 4 12:09:11 2021 .. Created module 11 | logLik: -1223402.66903597
#> Mon Oct 4 12:09:11 2021 .. Created module 12 | logLik: -1224026.19892208
#> Mon Oct 4 12:09:11 2021 .. Created module 13 | logLik: -1224675.63005464
#> Mon Oct 4 12:09:11 2021 .. Created module 14 | logLik: -1225317.91966369
#> Mon Oct 4 12:09:12 2021 .. Created module 15 | logLik: -1225971.50555157
#> Mon Oct 4 12:09:12 2021 .. Created module 16 | logLik: -1226557.7881506
#> Mon Oct 4 12:09:12 2021 .. Created module 17 | logLik: -1227080.13473523
#> Mon Oct 4 12:09:12 2021 .. Created module 18 | logLik: -1227603.99622355
#> Mon Oct 4 12:09:12 2021 .. Created module 19 | logLik: -1228247.84169741
#> Mon Oct 4 12:09:12 2021 .. Created module 20 | logLik: -1228828.70617002
#> Mon Oct 4 12:09:12 2021 .. Calculating perplexity
#> ==================================================
#> Completed recursive module splitting. Total time: 3.00991 secs
#> ==================================================
## Example results with perplexity plotGridSearchPerplexity(moduleSplit)
diff --git a/docs/reference/reorderCelda.html b/docs/reference/reorderCelda.html index 33d263bf..0775d4de 100644 --- a/docs/reference/reorderCelda.html +++ b/docs/reference/reorderCelda.html @@ -77,14 +77,14 @@ celda - 1.9.2 + 1.9.3
#> --------------------------------------------------
#> Starting Celda_C: Clustering cells.
#> --------------------------------------------------
#> Wed Sep 29 12:26:49 2021 .. Initializing 'z' in chain 1 with 'split'
#> Wed Sep 29 12:26:49 2021 .... Completed iteration: 1 | logLik: -1282027.27277705
#> Wed Sep 29 12:26:49 2021 .... Completed iteration: 2 | logLik: -1282027.27277705
#> Wed Sep 29 12:26:49 2021 .. Finished chain 1
#> --------------------------------------------------
#> Completed Celda_C. Total time: 0.07474399 secs
#> --------------------------------------------------
+
#> --------------------------------------------------
#> Starting Celda_C: Clustering cells.
#> --------------------------------------------------
#> Mon Oct 4 12:09:17 2021 .. Initializing 'z' in chain 1 with 'split'
#> Mon Oct 4 12:09:17 2021 .... Completed iteration: 1 | logLik: -1282027.27277705
#> Mon Oct 4 12:09:17 2021 .... Completed iteration: 2 | logLik: -1282027.27277705
#> Mon Oct 4 12:09:17 2021 .. Finished chain 1
#> --------------------------------------------------
#> Completed Celda_C. Total time: 0.06189203 secs
#> --------------------------------------------------
#> --------------------------------------------------
#> Starting Celda_CG: Clustering cells and genes.
#> --------------------------------------------------
#> Wed Sep 29 12:26:49 2021 .. Initializing 'z' in chain 1 with 'split'
#> Wed Sep 29 12:26:49 2021 .. Initializing 'y' in chain 1 with 'split'
#> Wed Sep 29 12:26:52 2021 .... Completed iteration: 1 | logLik: -1212891.16546068
#> Wed Sep 29 12:26:52 2021 .... Completed iteration: 2 | logLik: -1212891.16546068
#> Wed Sep 29 12:26:52 2021 .... Completed iteration: 3 | logLik: -1212891.16546068
#> Wed Sep 29 12:26:52 2021 .... Completed iteration: 4 | logLik: -1212891.16546068
#> Wed Sep 29 12:26:52 2021 .... Completed iteration: 5 | logLik: -1212891.16546068
#> Wed Sep 29 12:26:52 2021 .... Completed iteration: 6 | logLik: -1212891.16546068
#> Wed Sep 29 12:26:52 2021 .... Completed iteration: 7 | logLik: -1212891.16546068
#> Wed Sep 29 12:26:52 2021 .... Completed iteration: 8 | logLik: -1212891.16546068
#> Wed Sep 29 12:26:52 2021 .... Completed iteration: 9 | logLik: -1212891.16546068
#> Wed Sep 29 12:26:52 2021 .... Determining if any gene clusters should be split.
#> Wed Sep 29 12:26:52 2021 .... No additional splitting was performed.
#> Wed Sep 29 12:26:52 2021 .... Determining if any cell clusters should be split.
#> Wed Sep 29 12:26:52 2021 .... No additional splitting was performed.
#> Wed Sep 29 12:26:52 2021 .... Completed iteration: 10 | logLik: -1212891.16546068
#> Wed Sep 29 12:26:52 2021 .... Determining if any cell clusters should be split.
#> Wed Sep 29 12:26:52 2021 .... No additional splitting was performed.
#> Wed Sep 29 12:26:52 2021 .... Completed iteration: 11 | logLik: -1212891.16546068
#> Wed Sep 29 12:26:52 2021 .. Finished chain 1
#> --------------------------------------------------
#> Completed Celda_CG. Total time: 3.071206 secs
#> --------------------------------------------------
+
#> --------------------------------------------------
#> Starting Celda_CG: Clustering cells and genes.
#> --------------------------------------------------
#> Mon Oct 4 12:09:17 2021 .. Initializing 'z' in chain 1 with 'split'
#> Mon Oct 4 12:09:17 2021 .. Initializing 'y' in chain 1 with 'split'
#> Mon Oct 4 12:09:19 2021 .... Completed iteration: 1 | logLik: -1212891.16546068
#> Mon Oct 4 12:09:19 2021 .... Completed iteration: 2 | logLik: -1212891.16546068
#> Mon Oct 4 12:09:19 2021 .... Completed iteration: 3 | logLik: -1212891.16546068
#> Mon Oct 4 12:09:19 2021 .... Completed iteration: 4 | logLik: -1212891.16546068
#> Mon Oct 4 12:09:19 2021 .... Completed iteration: 5 | logLik: -1212891.16546068
#> Mon Oct 4 12:09:19 2021 .... Completed iteration: 6 | logLik: -1212891.16546068
#> Mon Oct 4 12:09:19 2021 .... Completed iteration: 7 | logLik: -1212891.16546068
#> Mon Oct 4 12:09:19 2021 .... Completed iteration: 8 | logLik: -1212891.16546068
#> Mon Oct 4 12:09:19 2021 .... Completed iteration: 9 | logLik: -1212891.16546068
#> Mon Oct 4 12:09:19 2021 .... Determining if any gene clusters should be split.
#> Mon Oct 4 12:09:19 2021 .... No additional splitting was performed.
#> Mon Oct 4 12:09:19 2021 .... Determining if any cell clusters should be split.
#> Mon Oct 4 12:09:19 2021 .... No additional splitting was performed.
#> Mon Oct 4 12:09:19 2021 .... Completed iteration: 10 | logLik: -1212891.16546068
#> Mon Oct 4 12:09:19 2021 .... Determining if any cell clusters should be split.
#> Mon Oct 4 12:09:20 2021 .... No additional splitting was performed.
#> Mon Oct 4 12:09:20 2021 .... Completed iteration: 11 | logLik: -1212891.16546068
#> Mon Oct 4 12:09:20 2021 .. Finished chain 1
#> --------------------------------------------------
#> Completed Celda_CG. Total time: 2.468526 secs
#> --------------------------------------------------
#> --------------------------------------------------
#> Starting Celda_G: Clustering genes.
#> --------------------------------------------------
#> Mon Oct 4 12:09:47 2021 .. Initializing 'y' in chain 1 with 'split'
#> Mon Oct 4 12:09:48 2021 .... Completed iteration: 1 | logLik: -289209.476865707
#> Mon Oct 4 12:09:48 2021 .... Completed iteration: 2 | logLik: -289209.476865707
#> Mon Oct 4 12:09:48 2021 .... Completed iteration: 3 | logLik: -289209.476865707
#> Mon Oct 4 12:09:48 2021 .... Completed iteration: 4 | logLik: -289209.476865707
#> Mon Oct 4 12:09:48 2021 .... Completed iteration: 5 | logLik: -289209.476865707
#> Mon Oct 4 12:09:48 2021 .... Completed iteration: 6 | logLik: -289209.476865707
#> Mon Oct 4 12:09:48 2021 .... Completed iteration: 7 | logLik: -289209.476865707
#> Mon Oct 4 12:09:48 2021 .... Completed iteration: 8 | logLik: -289209.476865707
#> Mon Oct 4 12:09:48 2021 .... Completed iteration: 9 | logLik: -289209.476865707
#> Mon Oct 4 12:09:48 2021 .... Determining if any gene clusters should be split.
#> Mon Oct 4 12:09:48 2021 .... No additional splitting was performed.
#> Mon Oct 4 12:09:48 2021 .... Completed iteration: 10 | logLik: -289209.476865707
#> Mon Oct 4 12:09:48 2021 .... Completed iteration: 11 | logLik: -289209.476865707
#> Mon Oct 4 12:09:48 2021 .. Finished chain 1
#> --------------------------------------------------
#> Completed Celda_G. Total time: 0.3001969 secs
#> --------------------------------------------------