diff --git a/DESCRIPTION b/DESCRIPTION index 93ec3e26..ac725b3b 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: celda Title: CEllular Latent Dirichlet Allocation -Version: 1.13.0 +Version: 1.12.0 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 fa6c3fe1..8d60c1ec 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,10 @@ +# celda v1.12.0 (2022-04-30) +* Update to match Bioconductor 3.15 release version + +# celda v1.11.1 (2022-03-31) +* Fixes to reports +* Use smoothe splines for perplexity and RPC plots + # celda v1.11.0 (2022-03-31) * Improvments to decontX vignette * Added ability to subsample to speed up perplexity calculations diff --git a/docs/404.html b/docs/404.html index bf7f6777..e44d423c 100644 --- a/docs/404.html +++ b/docs/404.html @@ -71,7 +71,7 @@ celda - 1.11.0 + 1.12.0 diff --git a/docs/CONDUCT.html b/docs/CONDUCT.html index 04960c1e..1b4c7f0d 100644 --- a/docs/CONDUCT.html +++ b/docs/CONDUCT.html @@ -71,7 +71,7 @@ celda - 1.11.0 + 1.12.0 diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index 3f4bb1dd..297cd487 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -71,7 +71,7 @@ celda - 1.11.0 + 1.12.0 diff --git a/docs/articles/articles/celda_pbmc3k.html b/docs/articles/articles/celda_pbmc3k.html index 61fdd5af..caf25edb 100644 --- a/docs/articles/articles/celda_pbmc3k.html +++ b/docs/articles/articles/celda_pbmc3k.html @@ -31,7 +31,7 @@ celda - 1.11.0 + 1.12.0 @@ -98,7 +98,7 @@

Celda - Analysis of PBMC3K

Joshua Campbell, Zhe Wang

-

Compiled March 31, 2022

+

Compiled April 30, 2022

Source: vignettes/articles/celda_pbmc3k.Rmd @@ -223,7 +223,7 @@

The perplexity alone often does not show a clear elbow or “leveling off”. However, the rate of perplexity change (RPC) can be more informative to determine when adding new modules does not add much additional information Zhao et al., 2015). An RPC closer to zero indicates that the addition of new modules or cell clusters is not substantially decreasing the perplexity. The RPC of models can be visualized using function plotRPC:

-plotRPC(moduleSplit, altExpName = altExpName, sep = 10, n = 30)
+plotRPC(moduleSplit, altExpName = altExpName)

In this case, we will choose an L of 80 as the RPC curve tends to level off at this point:

@@ -28248,7 +28248,7 @@ 

 
 # Plot differentially expressed genes that pass additional thresholds 'minClustExprPerc' and 'maxCtrlExprPerc'
 plotMarkerDiffExp(sce, topN = 5, log2fcThreshold = 0, rowLabel = TRUE, fdrThreshold = 0.05, minClustExprPerc = 0.6, maxCtrlExprPerc = 0.4, minMeanExpr = 0)

-

+

 
Other parameters such as minClustExprPerc (the minimum number of cells expressing the marker gene in the cluster) and maxCtrlExprPerc (the maximum number of cells expression the marker gene in other clusters) can be used to control how specific each marker gene is to each cell populations. Similarly, adding a log2 fold-change cutoff (e.g. 1) can select for markers that are more strongly up-regulated in a cell population.
@@ -28340,7 +28340,7 @@

## other attached packages: ## [1] scater_1.18.6 kableExtra_1.3.4 ## [3] knitr_1.31 ggplot2_3.3.5 -## [5] celda_1.11.0 singleCellTK_2.4.1 +## [5] celda_1.12.0 singleCellTK_2.5.1 ## [7] TENxPBMCData_1.8.0 HDF5Array_1.18.1 ## [9] rhdf5_2.34.0 DelayedArray_0.16.2 ## [11] Matrix_1.3-2 SingleCellExperiment_1.12.0 diff --git a/docs/articles/articles/celda_pbmc3k_files/figure-html/cell_clusters-1.png b/docs/articles/articles/celda_pbmc3k_files/figure-html/cell_clusters-1.png index fbf9ef95..9ae4ec07 100644 Binary files a/docs/articles/articles/celda_pbmc3k_files/figure-html/cell_clusters-1.png and b/docs/articles/articles/celda_pbmc3k_files/figure-html/cell_clusters-1.png differ diff --git a/docs/articles/articles/celda_pbmc3k_files/figure-html/cell_identities-1.png b/docs/articles/articles/celda_pbmc3k_files/figure-html/cell_identities-1.png index 5be37dbd..a4c26397 100644 Binary files a/docs/articles/articles/celda_pbmc3k_files/figure-html/cell_identities-1.png and b/docs/articles/articles/celda_pbmc3k_files/figure-html/cell_identities-1.png differ diff --git a/docs/articles/articles/celda_pbmc3k_files/figure-html/cell_split_perplexity-1.png b/docs/articles/articles/celda_pbmc3k_files/figure-html/cell_split_perplexity-1.png index 508a9592..6e46552e 100644 Binary files a/docs/articles/articles/celda_pbmc3k_files/figure-html/cell_split_perplexity-1.png and b/docs/articles/articles/celda_pbmc3k_files/figure-html/cell_split_perplexity-1.png differ diff --git a/docs/articles/articles/celda_pbmc3k_files/figure-html/cell_split_perplexity-2.png b/docs/articles/articles/celda_pbmc3k_files/figure-html/cell_split_perplexity-2.png index 77004a22..3759e044 100644 Binary files a/docs/articles/articles/celda_pbmc3k_files/figure-html/cell_split_perplexity-2.png and b/docs/articles/articles/celda_pbmc3k_files/figure-html/cell_split_perplexity-2.png differ diff --git a/docs/articles/articles/celda_pbmc3k_files/figure-html/diffExp_plot-1.png b/docs/articles/articles/celda_pbmc3k_files/figure-html/diffExp_plot-1.png index c7f564d5..6a29716b 100644 Binary files a/docs/articles/articles/celda_pbmc3k_files/figure-html/diffExp_plot-1.png and b/docs/articles/articles/celda_pbmc3k_files/figure-html/diffExp_plot-1.png differ diff --git a/docs/articles/articles/celda_pbmc3k_files/figure-html/module_split_perplexity-1.png b/docs/articles/articles/celda_pbmc3k_files/figure-html/module_split_perplexity-1.png index fbb14a45..0e53f063 100644 Binary files a/docs/articles/articles/celda_pbmc3k_files/figure-html/module_split_perplexity-1.png and b/docs/articles/articles/celda_pbmc3k_files/figure-html/module_split_perplexity-1.png differ diff --git a/docs/articles/articles/celda_pbmc3k_files/figure-html/module_split_rpc-1.png b/docs/articles/articles/celda_pbmc3k_files/figure-html/module_split_rpc-1.png index f878b77b..900a0c0a 100644 Binary files a/docs/articles/articles/celda_pbmc3k_files/figure-html/module_split_rpc-1.png and b/docs/articles/articles/celda_pbmc3k_files/figure-html/module_split_rpc-1.png differ diff --git a/docs/articles/articles/celda_pbmc3k_files/figure-html/sctk_qc_plot-1.png b/docs/articles/articles/celda_pbmc3k_files/figure-html/sctk_qc_plot-1.png index 060c792b..9391373c 100644 Binary files a/docs/articles/articles/celda_pbmc3k_files/figure-html/sctk_qc_plot-1.png and b/docs/articles/articles/celda_pbmc3k_files/figure-html/sctk_qc_plot-1.png differ diff --git a/docs/articles/articles/celda_pbmc3k_files/figure-html/sctk_qc_plot-2.png b/docs/articles/articles/celda_pbmc3k_files/figure-html/sctk_qc_plot-2.png index b3116aaa..24a260da 100644 Binary files a/docs/articles/articles/celda_pbmc3k_files/figure-html/sctk_qc_plot-2.png and b/docs/articles/articles/celda_pbmc3k_files/figure-html/sctk_qc_plot-2.png differ diff --git a/docs/articles/articles/celda_pbmc3k_files/figure-html/sctk_qc_plot-3.png b/docs/articles/articles/celda_pbmc3k_files/figure-html/sctk_qc_plot-3.png index 042eec75..44e97909 100644 Binary files a/docs/articles/articles/celda_pbmc3k_files/figure-html/sctk_qc_plot-3.png and b/docs/articles/articles/celda_pbmc3k_files/figure-html/sctk_qc_plot-3.png differ diff --git a/docs/articles/articles/celda_pbmc3k_files/figure-html/violin-1.png b/docs/articles/articles/celda_pbmc3k_files/figure-html/violin-1.png index 1f561d4d..a87b2c80 100644 Binary files a/docs/articles/articles/celda_pbmc3k_files/figure-html/violin-1.png and b/docs/articles/articles/celda_pbmc3k_files/figure-html/violin-1.png differ diff --git a/docs/articles/articles/decontX_pbmc4k.html b/docs/articles/articles/decontX_pbmc4k.html index 5bb44e5d..5b30e69a 100644 --- a/docs/articles/articles/decontX_pbmc4k.html +++ b/docs/articles/articles/decontX_pbmc4k.html @@ -31,7 +31,7 @@ celda - 1.11.0 + 1.12.0

@@ -106,7 +106,7 @@

Shiyi (Iris) Yang

Boston University School of Medicine
camp@bu.edu -

2022-03-31

+

2022-04-30

Source: vignettes/articles/decontX_pbmc4k.Rmd @@ -145,19 +145,12 @@

Load PBMC4k data from 10X

We will utilize the 10X PBMC 4K dataset as an example in this vignette. This data can be easily retrieved from the package TENxPBMCData. Make sure the the column names are set before running decontX.

-# Install TENxPBMCData if is it not already
-if (!requireNamespace("TENxPBMCData", quietly = TRUE)) {
-  if (!requireNamespace("BiocManager", quietly = TRUE)) {
-    install.packages("BiocManager")
-  }
-  BiocManager::install("TENxPBMCData")
-}
-
-# Load PBMC data
+# Load PBMC data
 library(TENxPBMCData)
 sce <- TENxPBMCData("pbmc4k")
 colnames(sce) <- paste(sce$Sample, sce$Barcode, sep = "_")
-rownames(sce) <- rowData(sce)$Symbol_TENx
+rownames(sce) <- rowData(sce)$Symbol_TENx +counts(sce) <- as(counts(sce), "dgCMatrix")

@@ -357,7 +350,7 @@

## [1] scater_1.18.6 ggplot2_3.3.5 ## [3] TENxPBMCData_1.8.0 HDF5Array_1.18.1 ## [5] rhdf5_2.34.0 DelayedArray_0.16.2 -## [7] celda_1.11.0 Matrix_1.3-2 +## [7] celda_1.12.0 Matrix_1.3-2 ## [9] SingleCellExperiment_1.12.0 SummarizedExperiment_1.20.0 ## [11] Biobase_2.50.0 GenomicRanges_1.42.0 ## [13] GenomeInfoDb_1.26.4 IRanges_2.24.1 diff --git a/docs/articles/articles/decontX_pbmc4k_files/figure-html/plot_decon-1.png b/docs/articles/articles/decontX_pbmc4k_files/figure-html/plot_decon-1.png index 73f65e3c..ec04a909 100644 Binary files a/docs/articles/articles/decontX_pbmc4k_files/figure-html/plot_decon-1.png and b/docs/articles/articles/decontX_pbmc4k_files/figure-html/plot_decon-1.png differ diff --git a/docs/articles/articles/decontX_pbmc4k_files/figure-html/plot_feature-1.png b/docs/articles/articles/decontX_pbmc4k_files/figure-html/plot_feature-1.png index 15f072f5..84886add 100644 Binary files a/docs/articles/articles/decontX_pbmc4k_files/figure-html/plot_feature-1.png and b/docs/articles/articles/decontX_pbmc4k_files/figure-html/plot_feature-1.png differ diff --git a/docs/articles/articles/decontX_pbmc4k_files/figure-html/plot_norm_counts-1.png b/docs/articles/articles/decontX_pbmc4k_files/figure-html/plot_norm_counts-1.png index 7f49ad42..0b467d1b 100644 Binary files a/docs/articles/articles/decontX_pbmc4k_files/figure-html/plot_norm_counts-1.png and b/docs/articles/articles/decontX_pbmc4k_files/figure-html/plot_norm_counts-1.png differ diff --git a/docs/articles/articles/installation.html b/docs/articles/articles/installation.html index e828a209..8be2a0fc 100644 --- a/docs/articles/articles/installation.html +++ b/docs/articles/articles/installation.html @@ -31,7 +31,7 @@ celda - 1.11.0 + 1.12.0

diff --git a/docs/articles/celda.html b/docs/articles/celda.html index 20d8af81..5414c80a 100644 --- a/docs/articles/celda.html +++ b/docs/articles/celda.html @@ -31,7 +31,7 @@ celda - 1.11.0 + 1.12.0 @@ -107,7 +107,7 @@

Zhe Wang

Boston University School of Medicine

Yusuke Koga

- Boston University School of Medicine

2022-03-31

+ Boston University School of Medicine

2022-04-30

Source: vignettes/celda.Rmd @@ -389,7 +389,7 @@

## [8] methods base ## ## other attached packages: -## [1] celda_1.11.0 Matrix_1.3-2 +## [1] celda_1.12.0 Matrix_1.3-2 ## [3] SingleCellExperiment_1.12.0 SummarizedExperiment_1.20.0 ## [5] Biobase_2.50.0 GenomicRanges_1.42.0 ## [7] GenomeInfoDb_1.26.4 IRanges_2.24.1 diff --git a/docs/articles/celda_files/figure-html/celda_heatmap-1.png b/docs/articles/celda_files/figure-html/celda_heatmap-1.png index 1e4919df..a3e364ee 100644 Binary files a/docs/articles/celda_files/figure-html/celda_heatmap-1.png and b/docs/articles/celda_files/figure-html/celda_heatmap-1.png differ diff --git a/docs/articles/celda_files/figure-html/module_heatmap-1.png b/docs/articles/celda_files/figure-html/module_heatmap-1.png index 22049db4..73b985ab 100644 Binary files a/docs/articles/celda_files/figure-html/module_heatmap-1.png and b/docs/articles/celda_files/figure-html/module_heatmap-1.png differ diff --git a/docs/articles/celda_files/figure-html/module_split_rpc-1.png b/docs/articles/celda_files/figure-html/module_split_rpc-1.png index b3e195df..4bf95fa0 100644 Binary files a/docs/articles/celda_files/figure-html/module_split_rpc-1.png and b/docs/articles/celda_files/figure-html/module_split_rpc-1.png differ diff --git a/docs/articles/celda_files/figure-html/plot_grid_search-1.png b/docs/articles/celda_files/figure-html/plot_grid_search-1.png index 8799440d..f95fbb9f 100644 Binary files a/docs/articles/celda_files/figure-html/plot_grid_search-1.png and b/docs/articles/celda_files/figure-html/plot_grid_search-1.png differ diff --git a/docs/articles/celda_files/figure-html/plot_umap-2.png b/docs/articles/celda_files/figure-html/plot_umap-2.png index f3b97757..da42f0ed 100644 Binary files a/docs/articles/celda_files/figure-html/plot_umap-2.png and b/docs/articles/celda_files/figure-html/plot_umap-2.png differ diff --git a/docs/articles/celda_files/figure-html/plot_umap-3.png b/docs/articles/celda_files/figure-html/plot_umap-3.png index 6b37abc6..cde8aeec 100644 Binary files a/docs/articles/celda_files/figure-html/plot_umap-3.png and b/docs/articles/celda_files/figure-html/plot_umap-3.png differ diff --git a/docs/articles/celda_files/figure-html/propmap-1.png b/docs/articles/celda_files/figure-html/propmap-1.png index 51145ed4..d6496027 100644 Binary files a/docs/articles/celda_files/figure-html/propmap-1.png and b/docs/articles/celda_files/figure-html/propmap-1.png differ diff --git a/docs/articles/celda_files/figure-html/rpc_cell-1.png b/docs/articles/celda_files/figure-html/rpc_cell-1.png index 8060c0be..001faf83 100644 Binary files a/docs/articles/celda_files/figure-html/rpc_cell-1.png and b/docs/articles/celda_files/figure-html/rpc_cell-1.png differ diff --git a/docs/articles/celda_files/figure-html/rpc_cell-2.png b/docs/articles/celda_files/figure-html/rpc_cell-2.png index 9732ba5b..f287e381 100644 Binary files a/docs/articles/celda_files/figure-html/rpc_cell-2.png and b/docs/articles/celda_files/figure-html/rpc_cell-2.png differ diff --git a/docs/articles/celda_files/figure-html/unnamed-chunk-3-1.png b/docs/articles/celda_files/figure-html/unnamed-chunk-3-1.png index 68e0d5fb..f5fc8f6e 100644 Binary files a/docs/articles/celda_files/figure-html/unnamed-chunk-3-1.png and b/docs/articles/celda_files/figure-html/unnamed-chunk-3-1.png differ diff --git a/docs/articles/decontX.html b/docs/articles/decontX.html index d9366eb1..1358d2da 100644 --- a/docs/articles/decontX.html +++ b/docs/articles/decontX.html @@ -31,7 +31,7 @@ celda - 1.11.0 + 1.12.0 @@ -106,7 +106,7 @@

Shiyi (Iris) Yang

Boston University School of Medicine
-

2022-03-31

+

2022-04-30

Source: vignettes/decontX.Rmd @@ -145,19 +145,12 @@

Load PBMC4k data from 10X

We will utilize the 10X PBMC 4K dataset as an example in this vignette. This data can be easily retrieved from the package TENxPBMCData. Make sure the the column names are set before running decontX.

-# Install TENxPBMCData if is it not already
-if (!requireNamespace("TENxPBMCData", quietly = TRUE)) {
-  if (!requireNamespace("BiocManager", quietly = TRUE)) {
-    install.packages("BiocManager")
-  }
-  BiocManager::install("TENxPBMCData")
-}
-
-# Load PBMC data
+# Load PBMC data
 library(TENxPBMCData)
 sce <- TENxPBMCData("pbmc4k")
 colnames(sce) <- paste(sce$Sample, sce$Barcode, sep = "_")
-rownames(sce) <- rowData(sce)$Symbol_TENx
+rownames(sce) <- rowData(sce)$Symbol_TENx +counts(sce) <- as(counts(sce), "dgCMatrix")

@@ -357,7 +350,7 @@

## [1] scater_1.18.6 ggplot2_3.3.5 ## [3] TENxPBMCData_1.8.0 HDF5Array_1.18.1 ## [5] rhdf5_2.34.0 DelayedArray_0.16.2 -## [7] celda_1.11.0 Matrix_1.3-2 +## [7] celda_1.12.0 Matrix_1.3-2 ## [9] SingleCellExperiment_1.12.0 SummarizedExperiment_1.20.0 ## [11] Biobase_2.50.0 GenomicRanges_1.42.0 ## [13] GenomeInfoDb_1.26.4 IRanges_2.24.1 diff --git a/docs/articles/decontX_files/figure-html/plot_decon-1.png b/docs/articles/decontX_files/figure-html/plot_decon-1.png index 73f65e3c..ec04a909 100644 Binary files a/docs/articles/decontX_files/figure-html/plot_decon-1.png and b/docs/articles/decontX_files/figure-html/plot_decon-1.png differ diff --git a/docs/articles/decontX_files/figure-html/plot_feature-1.png b/docs/articles/decontX_files/figure-html/plot_feature-1.png index 15f072f5..84886add 100644 Binary files a/docs/articles/decontX_files/figure-html/plot_feature-1.png and b/docs/articles/decontX_files/figure-html/plot_feature-1.png differ diff --git a/docs/articles/decontX_files/figure-html/plot_norm_counts-1.png b/docs/articles/decontX_files/figure-html/plot_norm_counts-1.png index 7f49ad42..0b467d1b 100644 Binary files a/docs/articles/decontX_files/figure-html/plot_norm_counts-1.png and b/docs/articles/decontX_files/figure-html/plot_norm_counts-1.png differ diff --git a/docs/articles/index.html b/docs/articles/index.html index 797fcce6..609b51b1 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -71,7 +71,7 @@ celda - 1.11.0 + 1.12.0

diff --git a/docs/authors.html b/docs/authors.html index 7899c5c5..7b484aaa 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -71,7 +71,7 @@ celda - 1.11.0 + 1.12.0 diff --git a/docs/index.html b/docs/index.html index 07b78e6a..fefe595d 100644 --- a/docs/index.html +++ b/docs/index.html @@ -37,7 +37,7 @@ celda - 1.11.0 + 1.12.0 @@ -112,9 +112,12 @@ 

if (!requireNamespace("BiocManager", quietly = TRUE))
     install.packages("BiocManager")
 BiocManager::install("celda")
-

To install the development version (R >= 3.6) of celda from GitHub using devtools:

+

The latest stable version of celda can be installed from GitHub using devtools:

library(devtools)
 install_github("campbio/celda")
+

The development version of celda can also be installed from GitHub using devtools:

+
library(devtools)
+install_github("campbio/celda@devel")

NOTE For MAC OSX users, devtools::install_github() requires installation of libgit2. This can be installed via homebrew:

brew install libgit2

Also, if you receive installation errors when Rcpp is being installed and compiled, try following the steps outlined here to solve the issue:

diff --git a/docs/news/index.html b/docs/news/index.html index 5ce5c67a..76e32ba5 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -71,7 +71,7 @@ celda - 1.11.0 + 1.12.0 @@ -138,14 +138,36 @@

Changelog

Source: NEWS.md -
+
+

+celda v1.12.0 (2022-03-31)

+
    +
  • Update to match Bioconductor 3.15 release version
    • +
+
+
+

+celda v1.11.1 (2022-03-31)

+
    +
  • Fixes to reports
    • +
  • Use smoothe splines for perplexity and RPC plots
    • +
+
+

-celda v1.11.0 (2022-XX-XX)

+celda v1.11.0 (2022-03-31)
  • Improvments to decontX vignette
  • Added ability to subsample to speed up perplexity calculations
  • Added ability to use batch parameter with the raw matrix in decontX
+
+
+

+celda v1.10.0 (2021-12-28)

+
    +
  • Update to match Bioconductor release version
    • +

diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 5dd09109..8205e574 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: 2022-03-31T15:09Z +last_built: 2022-04-30T19:13Z diff --git a/docs/reference/Rplot002.png b/docs/reference/Rplot002.png index 7a5a366f..c898a4b0 100644 Binary files a/docs/reference/Rplot002.png and b/docs/reference/Rplot002.png differ diff --git a/docs/reference/Rplot003.png b/docs/reference/Rplot003.png index 154f772f..42bb7c88 100644 Binary files a/docs/reference/Rplot003.png and b/docs/reference/Rplot003.png differ diff --git a/docs/reference/Rplot004.png b/docs/reference/Rplot004.png index f2534aa5..b32dd758 100644 Binary files a/docs/reference/Rplot004.png and b/docs/reference/Rplot004.png differ diff --git a/docs/reference/appendCeldaList.html b/docs/reference/appendCeldaList.html index 8034e4cd..f1274760 100644 --- a/docs/reference/appendCeldaList.html +++ b/docs/reference/appendCeldaList.html @@ -73,7 +73,7 @@ celda - 1.11.0 + 1.12.0

diff --git a/docs/reference/availableModels.html b/docs/reference/availableModels.html index 1a9e46f0..7ce89121 100644 --- a/docs/reference/availableModels.html +++ b/docs/reference/availableModels.html @@ -72,7 +72,7 @@ celda - 1.11.0 + 1.12.0
diff --git a/docs/reference/bestLogLikelihood.html b/docs/reference/bestLogLikelihood.html index 81c67055..4e448bd6 100644 --- a/docs/reference/bestLogLikelihood.html +++ b/docs/reference/bestLogLikelihood.html @@ -73,7 +73,7 @@ celda - 1.11.0 + 1.12.0 diff --git a/docs/reference/celda.html b/docs/reference/celda.html index bb1aee7b..d8c29748 100644 --- a/docs/reference/celda.html +++ b/docs/reference/celda.html @@ -72,7 +72,7 @@ celda - 1.11.0 + 1.12.0 diff --git a/docs/reference/celdaCGGridSearchRes.html b/docs/reference/celdaCGGridSearchRes.html index 586631aa..60d65d30 100644 --- a/docs/reference/celdaCGGridSearchRes.html +++ b/docs/reference/celdaCGGridSearchRes.html @@ -72,7 +72,7 @@ celda - 1.11.0 + 1.12.0 diff --git a/docs/reference/celdaCGMod.html b/docs/reference/celdaCGMod.html index f5e482db..0e6acfc6 100644 --- a/docs/reference/celdaCGMod.html +++ b/docs/reference/celdaCGMod.html @@ -73,7 +73,7 @@ celda - 1.11.0 + 1.12.0 diff --git a/docs/reference/celdaCGSim.html b/docs/reference/celdaCGSim.html index f6af63d0..593e79d5 100644 --- a/docs/reference/celdaCGSim.html +++ b/docs/reference/celdaCGSim.html @@ -73,7 +73,7 @@ celda - 1.11.0 + 1.12.0 diff --git a/docs/reference/celdaCMod.html b/docs/reference/celdaCMod.html index 2212047d..23d0b821 100644 --- a/docs/reference/celdaCMod.html +++ b/docs/reference/celdaCMod.html @@ -72,7 +72,7 @@ celda - 1.11.0 + 1.12.0 diff --git a/docs/reference/celdaCSim.html b/docs/reference/celdaCSim.html index e0a8c3b8..6d0647d1 100644 --- a/docs/reference/celdaCSim.html +++ b/docs/reference/celdaCSim.html @@ -72,7 +72,7 @@ celda - 1.11.0 + 1.12.0 diff --git a/docs/reference/celdaClusters.html b/docs/reference/celdaClusters.html index 181d1474..c286ef5d 100644 --- a/docs/reference/celdaClusters.html +++ b/docs/reference/celdaClusters.html @@ -77,7 +77,7 @@ celda - 1.11.0 + 1.12.0 diff --git a/docs/reference/celdaGMod.html b/docs/reference/celdaGMod.html index dd591303..cbb210c7 100644 --- a/docs/reference/celdaGMod.html +++ b/docs/reference/celdaGMod.html @@ -72,7 +72,7 @@ celda - 1.11.0 + 1.12.0 diff --git a/docs/reference/celdaGSim.html b/docs/reference/celdaGSim.html index cee77863..fc8c5cb4 100644 --- a/docs/reference/celdaGSim.html +++ b/docs/reference/celdaGSim.html @@ -72,7 +72,7 @@ celda - 1.11.0 + 1.12.0 diff --git a/docs/reference/celdaGridSearch.html b/docs/reference/celdaGridSearch.html index e2951693..c5699ac5 100644 --- a/docs/reference/celdaGridSearch.html +++ b/docs/reference/celdaGridSearch.html @@ -79,7 +79,7 @@ celda - 1.11.0 + 1.12.0 diff --git a/docs/reference/celdaHeatmap.html b/docs/reference/celdaHeatmap.html index 63936ab1..1799e36a 100644 --- a/docs/reference/celdaHeatmap.html +++ b/docs/reference/celdaHeatmap.html @@ -73,7 +73,7 @@ celda - 1.11.0 + 1.12.0 diff --git a/docs/reference/celdaModel.html b/docs/reference/celdaModel.html index 8cc34609..40017af0 100644 --- a/docs/reference/celdaModel.html +++ b/docs/reference/celdaModel.html @@ -75,7 +75,7 @@ celda - 1.11.0 + 1.12.0 diff --git a/docs/reference/celdaModules.html b/docs/reference/celdaModules.html index 027a7952..e9ba2599 100644 --- a/docs/reference/celdaModules.html +++ b/docs/reference/celdaModules.html @@ -75,7 +75,7 @@ celda - 1.11.0 + 1.12.0 diff --git a/docs/reference/celdaPerplexity-celdaList-method.html b/docs/reference/celdaPerplexity-celdaList-method.html index 67aecdfc..1bd056a4 100644 --- a/docs/reference/celdaPerplexity-celdaList-method.html +++ b/docs/reference/celdaPerplexity-celdaList-method.html @@ -73,7 +73,7 @@ celda - 1.11.0 + 1.12.0 diff --git a/docs/reference/celdaPerplexity.html b/docs/reference/celdaPerplexity.html index 56eff0d1..b6fcc63e 100644 --- a/docs/reference/celdaPerplexity.html +++ b/docs/reference/celdaPerplexity.html @@ -73,7 +73,7 @@ celda - 1.11.0 + 1.12.0 diff --git a/docs/reference/celdaProbabilityMap.html b/docs/reference/celdaProbabilityMap.html index 9f188a7d..795e6661 100644 --- a/docs/reference/celdaProbabilityMap.html +++ b/docs/reference/celdaProbabilityMap.html @@ -74,7 +74,7 @@ celda - 1.11.0 + 1.12.0 diff --git a/docs/reference/celdaTsne.html b/docs/reference/celdaTsne.html index 0e771162..58206848 100644 --- a/docs/reference/celdaTsne.html +++ b/docs/reference/celdaTsne.html @@ -79,7 +79,7 @@ celda - 1.11.0 + 1.12.0 diff --git a/docs/reference/celdaUmap.html b/docs/reference/celdaUmap.html index e3b30c2b..eb5c6e0d 100644 --- a/docs/reference/celdaUmap.html +++ b/docs/reference/celdaUmap.html @@ -79,7 +79,7 @@ celda - 1.11.0 + 1.12.0 diff --git a/docs/reference/celda_C.html b/docs/reference/celda_C.html index 09600c66..09a25b42 100644 --- a/docs/reference/celda_C.html +++ b/docs/reference/celda_C.html @@ -78,7 +78,7 @@ celda - 1.11.0 + 1.12.0 @@ -357,7 +357,7 @@

Examp K = celdaCSim$K, sampleLabel = celdaCSim$sampleLabel, nchains = 1) -
#> --------------------------------------------------
#> Starting Celda_C: Clustering cells.
#> --------------------------------------------------
#> Thu Mar 31 11:10:16 2022 .. Initializing 'z' in chain 1 with 'split'
#> Thu Mar 31 11:10:16 2022 .... Completed iteration: 1 | logLik: -1282027.27277705
#> Thu Mar 31 11:10:16 2022 .... Completed iteration: 2 | logLik: -1282027.27277705
#> Thu Mar 31 11:10:16 2022 .. Finished chain 1
#> --------------------------------------------------
#> Completed Celda_C. Total time: 0.1379719 secs
#> --------------------------------------------------
+
#> --------------------------------------------------
#> Starting Celda_C: Clustering cells.
#> --------------------------------------------------
#> Sat Apr 30 15:14:05 2022 .. Initializing 'z' in chain 1 with 'split'
#> Sat Apr 30 15:14:06 2022 .... Completed iteration: 1 | logLik: -1282027.27277705
#> Sat Apr 30 15:14:06 2022 .... Completed iteration: 2 | logLik: -1282027.27277705
#> Sat Apr 30 15:14:06 2022 .. Finished chain 1
#> --------------------------------------------------
#> Completed Celda_C. Total time: 0.149879 secs
#> --------------------------------------------------
@@ -402,7 +402,7 @@

Examp L = celdaCGSim$L, sampleLabel = celdaCGSim$sampleLabel, nchains = 1) -
#> --------------------------------------------------
#> Starting Celda_CG: Clustering cells and genes.
#> --------------------------------------------------
#> Thu Mar 31 11:10:17 2022 .. Initializing 'z' in chain 1 with 'split'
#> Thu Mar 31 11:10:17 2022 .. Initializing 'y' in chain 1 with 'split'
#> Thu Mar 31 11:10:19 2022 .... Completed iteration: 1 | logLik: -1215542.98684529
#> Thu Mar 31 11:10:19 2022 .... Completed iteration: 2 | logLik: -1215541.0958389
#> Thu Mar 31 11:10:19 2022 .... Completed iteration: 3 | logLik: -1215541.0958389
#> Thu Mar 31 11:10:19 2022 .... Completed iteration: 4 | logLik: -1215542.98684529
#> Thu Mar 31 11:10:19 2022 .... Completed iteration: 5 | logLik: -1215541.0958389
#> Thu Mar 31 11:10:19 2022 .... Completed iteration: 6 | logLik: -1215541.0958389
#> Thu Mar 31 11:10:19 2022 .... Completed iteration: 7 | logLik: -1215541.0958389
#> Thu Mar 31 11:10:19 2022 .... Completed iteration: 8 | logLik: -1215541.0958389
#> Thu Mar 31 11:10:19 2022 .... Completed iteration: 9 | logLik: -1215541.0958389
#> Thu Mar 31 11:10:19 2022 .... Determining if any gene clusters should be split.
#> Thu Mar 31 11:10:20 2022 .... No additional splitting was performed.
#> Thu Mar 31 11:10:20 2022 .... Determining if any cell clusters should be split.
#> Thu Mar 31 11:10:20 2022 .... No additional splitting was performed.
#> Thu Mar 31 11:10:20 2022 .... Completed iteration: 10 | logLik: -1215541.0958389
#> Thu Mar 31 11:10:20 2022 .... Determining if any cell clusters should be split.
#> Thu Mar 31 11:10:20 2022 .... No additional splitting was performed.
#> Thu Mar 31 11:10:20 2022 .... Completed iteration: 11 | logLik: -1215541.0958389
#> Thu Mar 31 11:10:20 2022 .. Finished chain 1
#> --------------------------------------------------
#> Completed Celda_CG. Total time: 3.212025 secs
#> --------------------------------------------------
+
#> --------------------------------------------------
#> Starting Celda_CG: Clustering cells and genes.
#> --------------------------------------------------
#> Sat Apr 30 15:14:06 2022 .. Initializing 'z' in chain 1 with 'split'
#> Sat Apr 30 15:14:06 2022 .. Initializing 'y' in chain 1 with 'split'
#> Sat Apr 30 15:14:09 2022 .... Completed iteration: 1 | logLik: -1215542.98684529
#> Sat Apr 30 15:14:09 2022 .... Completed iteration: 2 | logLik: -1215541.0958389
#> Sat Apr 30 15:14:09 2022 .... Completed iteration: 3 | logLik: -1215541.0958389
#> Sat Apr 30 15:14:09 2022 .... Completed iteration: 4 | logLik: -1215542.98684529
#> Sat Apr 30 15:14:09 2022 .... Completed iteration: 5 | logLik: -1215541.0958389
#> Sat Apr 30 15:14:09 2022 .... Completed iteration: 6 | logLik: -1215541.0958389
#> Sat Apr 30 15:14:09 2022 .... Completed iteration: 7 | logLik: -1215541.0958389
#> Sat Apr 30 15:14:09 2022 .... Completed iteration: 8 | logLik: -1215541.0958389
#> Sat Apr 30 15:14:09 2022 .... Completed iteration: 9 | logLik: -1215541.0958389
#> Sat Apr 30 15:14:09 2022 .... Determining if any gene clusters should be split.
#> Sat Apr 30 15:14:09 2022 .... No additional splitting was performed.
#> Sat Apr 30 15:14:09 2022 .... Determining if any cell clusters should be split.
#> Sat Apr 30 15:14:09 2022 .... No additional splitting was performed.
#> Sat Apr 30 15:14:09 2022 .... Completed iteration: 10 | logLik: -1215541.0958389
#> Sat Apr 30 15:14:09 2022 .... Determining if any cell clusters should be split.
#> Sat Apr 30 15:14:09 2022 .... No additional splitting was performed.
#> Sat Apr 30 15:14:09 2022 .... Completed iteration: 11 | logLik: -1215541.0958389
#> Sat Apr 30 15:14:09 2022 .. Finished chain 1
#> --------------------------------------------------
#> Completed Celda_CG. Total time: 3.036642 secs
#> --------------------------------------------------
@@ -341,7 +341,7 @@

See a

Examples

data(celdaGSim)
 sce <- celda_G(celdaGSim$counts, L = celdaGSim$L, nchains = 1)
-
#> --------------------------------------------------
#> Starting Celda_G: Clustering genes.
#> --------------------------------------------------
#> Thu Mar 31 11:10:20 2022 .. Initializing 'y' in chain 1 with 'split' 
#> Thu Mar 31 11:10:22 2022 .... Completed iteration: 1 | logLik: -290669.046132139
#> Thu Mar 31 11:10:22 2022 .... Completed iteration: 2 | logLik: -290669.046132139
#> Thu Mar 31 11:10:22 2022 .... Completed iteration: 3 | logLik: -290669.046132139
#> Thu Mar 31 11:10:22 2022 .... Completed iteration: 4 | logLik: -290669.046132139
#> Thu Mar 31 11:10:22 2022 .... Completed iteration: 5 | logLik: -290669.046132139
#> Thu Mar 31 11:10:22 2022 .... Completed iteration: 6 | logLik: -290669.046132139
#> Thu Mar 31 11:10:22 2022 .... Completed iteration: 7 | logLik: -290669.046132139
#> Thu Mar 31 11:10:22 2022 .... Completed iteration: 8 | logLik: -290669.046132139
#> Thu Mar 31 11:10:22 2022 .... Completed iteration: 9 | logLik: -290669.046132139
#> Thu Mar 31 11:10:22 2022 .... Determining if any gene clusters should be split.
#> Thu Mar 31 11:10:22 2022 .... No additional splitting was performed.
#> Thu Mar 31 11:10:22 2022 .... Completed iteration: 10 | logLik: -290669.046132139
#> Thu Mar 31 11:10:22 2022 .... Completed iteration: 11 | logLik: -290669.046132139
#> Thu Mar 31 11:10:22 2022 .. Finished chain 1
#> --------------------------------------------------
#> Completed Celda_G. Total time: 2.057198 secs
#> --------------------------------------------------
+
#> --------------------------------------------------
#> Starting Celda_G: Clustering genes.
#> --------------------------------------------------
#> Sat Apr 30 15:14:09 2022 .. Initializing 'y' in chain 1 with 'split'
#> Sat Apr 30 15:14:11 2022 .... Completed iteration: 1 | logLik: -290669.046132139
#> Sat Apr 30 15:14:11 2022 .... Completed iteration: 2 | logLik: -290669.046132139
#> Sat Apr 30 15:14:11 2022 .... Completed iteration: 3 | logLik: -290669.046132139
#> Sat Apr 30 15:14:11 2022 .... Completed iteration: 4 | logLik: -290669.046132139
#> Sat Apr 30 15:14:11 2022 .... Completed iteration: 5 | logLik: -290669.046132139
#> Sat Apr 30 15:14:11 2022 .... Completed iteration: 6 | logLik: -290669.046132139
#> Sat Apr 30 15:14:11 2022 .... Completed iteration: 7 | logLik: -290669.046132139
#> Sat Apr 30 15:14:11 2022 .... Completed iteration: 8 | logLik: -290669.046132139
#> Sat Apr 30 15:14:11 2022 .... Completed iteration: 9 | logLik: -290669.046132139
#> Sat Apr 30 15:14:11 2022 .... Determining if any gene clusters should be split.
#> Sat Apr 30 15:14:11 2022 .... No additional splitting was performed.
#> Sat Apr 30 15:14:11 2022 .... Completed iteration: 10 | logLik: -290669.046132139
#> Sat Apr 30 15:14:11 2022 .... Completed iteration: 11 | logLik: -290669.046132139
#> Sat Apr 30 15:14:11 2022 .. Finished chain 1
#> --------------------------------------------------
#> Completed Celda_G. Total time: 2.014838 secs
#> --------------------------------------------------
diff --git a/docs/reference/clusterProbability.html b/docs/reference/clusterProbability.html index 21e32ea8..98236f2a 100644 --- a/docs/reference/clusterProbability.html +++ b/docs/reference/clusterProbability.html @@ -77,7 +77,7 @@ celda - 1.11.0 + 1.12.0 diff --git a/docs/reference/compareCountMatrix.html b/docs/reference/compareCountMatrix.html index 6b062aad..f6b660b0 100644 --- a/docs/reference/compareCountMatrix.html +++ b/docs/reference/compareCountMatrix.html @@ -73,7 +73,7 @@ celda - 1.11.0 + 1.12.0 diff --git a/docs/reference/contaminationSim.html b/docs/reference/contaminationSim.html index bcd044a3..8fe6eb51 100644 --- a/docs/reference/contaminationSim.html +++ b/docs/reference/contaminationSim.html @@ -73,7 +73,7 @@ celda - 1.11.0 + 1.12.0 diff --git a/docs/reference/countChecksum-celdaList-method.html b/docs/reference/countChecksum-celdaList-method.html index ed659b50..e9180a48 100644 --- a/docs/reference/countChecksum-celdaList-method.html +++ b/docs/reference/countChecksum-celdaList-method.html @@ -73,7 +73,7 @@ celda - 1.11.0 + 1.12.0 diff --git a/docs/reference/countChecksum.html b/docs/reference/countChecksum.html index 060e06b3..9379e3ce 100644 --- a/docs/reference/countChecksum.html +++ b/docs/reference/countChecksum.html @@ -73,7 +73,7 @@ celda - 1.11.0 + 1.12.0 diff --git a/docs/reference/decontX.html b/docs/reference/decontX.html index 8e2dcdca..d503afb3 100644 --- a/docs/reference/decontX.html +++ b/docs/reference/decontX.html @@ -73,7 +73,7 @@ celda - 1.11.0 + 1.12.0 @@ -351,7 +351,7 @@

Examp library(SingleCellExperiment) sce <- SingleCellExperiment(list(counts = s$observedCounts)) sce <- decontX(sce) -
#> --------------------------------------------------
#> Starting DecontX
#> --------------------------------------------------
#> Thu Mar 31 11:10:24 2022 .. Analyzing all cells
#> Thu Mar 31 11:10:24 2022 .... Converting to sparse matrix
#> Thu Mar 31 11:10:24 2022 .... Generating UMAP and estimating cell types
#> Thu Mar 31 11:10:27 2022 .... Estimating contamination
#> Thu Mar 31 11:10:27 2022 ...... Completed iteration: 9 | converge: 0.0009154
#> Thu Mar 31 11:10:27 2022 .. Calculating final decontaminated matrix
#> --------------------------------------------------
#> Completed DecontX. Total time: 2.832404 secs
#> --------------------------------------------------
+
#> --------------------------------------------------
#> Starting DecontX
#> --------------------------------------------------
#> Sat Apr 30 15:14:13 2022 .. Analyzing all cells
#> Sat Apr 30 15:14:13 2022 .... Converting to sparse matrix
#> Sat Apr 30 15:14:13 2022 .... Generating UMAP and estimating cell types
#> Sat Apr 30 15:14:16 2022 .... Estimating contamination
#> Sat Apr 30 15:14:16 2022 ...... Completed iteration: 9 | converge: 0.0009154
#> Sat Apr 30 15:14:16 2022 .. Calculating final decontaminated matrix
#> --------------------------------------------------
#> Completed DecontX. Total time: 2.671371 secs
#> --------------------------------------------------
# Plot contamination on UMAP plotDecontXContamination(sce)
diff --git a/docs/reference/decontXcounts.html b/docs/reference/decontXcounts.html index 892d026b..257dce67 100644 --- a/docs/reference/decontXcounts.html +++ b/docs/reference/decontXcounts.html @@ -73,7 +73,7 @@ celda - 1.11.0 + 1.12.0
diff --git a/docs/reference/distinctColors.html b/docs/reference/distinctColors.html index 645f1ec3..217ff90e 100644 --- a/docs/reference/distinctColors.html +++ b/docs/reference/distinctColors.html @@ -72,7 +72,7 @@ celda - 1.11.0 + 1.12.0 diff --git a/docs/reference/eigenMatMultInt.html b/docs/reference/eigenMatMultInt.html index 3a1f1a5d..4d9c2739 100644 --- a/docs/reference/eigenMatMultInt.html +++ b/docs/reference/eigenMatMultInt.html @@ -72,7 +72,7 @@ celda - 1.11.0 + 1.12.0 diff --git a/docs/reference/eigenMatMultNumeric.html b/docs/reference/eigenMatMultNumeric.html index 4e7993f6..5fad41cd 100644 --- a/docs/reference/eigenMatMultNumeric.html +++ b/docs/reference/eigenMatMultNumeric.html @@ -72,7 +72,7 @@ celda - 1.11.0 + 1.12.0 diff --git a/docs/reference/factorizeMatrix.html b/docs/reference/factorizeMatrix.html index 6fb9b375..817b421a 100644 --- a/docs/reference/factorizeMatrix.html +++ b/docs/reference/factorizeMatrix.html @@ -75,7 +75,7 @@ celda - 1.11.0 + 1.12.0 diff --git a/docs/reference/fastNormProp.html b/docs/reference/fastNormProp.html index 343c0b8a..16552001 100644 --- a/docs/reference/fastNormProp.html +++ b/docs/reference/fastNormProp.html @@ -72,7 +72,7 @@ celda - 1.11.0 + 1.12.0 diff --git a/docs/reference/fastNormPropLog.html b/docs/reference/fastNormPropLog.html index 1e7135c2..755ebe51 100644 --- a/docs/reference/fastNormPropLog.html +++ b/docs/reference/fastNormPropLog.html @@ -72,7 +72,7 @@ celda - 1.11.0 + 1.12.0 diff --git a/docs/reference/fastNormPropSqrt.html b/docs/reference/fastNormPropSqrt.html index 564af63e..2e2ec795 100644 --- a/docs/reference/fastNormPropSqrt.html +++ b/docs/reference/fastNormPropSqrt.html @@ -72,7 +72,7 @@ celda - 1.11.0 + 1.12.0 diff --git a/docs/reference/featureModuleLookup.html b/docs/reference/featureModuleLookup.html index 85c1d249..320dde6c 100644 --- a/docs/reference/featureModuleLookup.html +++ b/docs/reference/featureModuleLookup.html @@ -74,7 +74,7 @@ celda - 1.11.0 + 1.12.0 diff --git a/docs/reference/featureModuleTable.html b/docs/reference/featureModuleTable.html index 403280dc..4ca9d219 100644 --- a/docs/reference/featureModuleTable.html +++ b/docs/reference/featureModuleTable.html @@ -73,7 +73,7 @@ celda - 1.11.0 + 1.12.0 diff --git a/docs/reference/geneSetEnrich.html b/docs/reference/geneSetEnrich.html index a2456758..e0978c01 100644 --- a/docs/reference/geneSetEnrich.html +++ b/docs/reference/geneSetEnrich.html @@ -75,7 +75,7 @@ celda - 1.11.0 + 1.12.0 diff --git a/docs/reference/index.html b/docs/reference/index.html index da0093d8..a06c0842 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -71,7 +71,7 @@ celda - 1.11.0 + 1.12.0 diff --git a/docs/reference/logLikelihood.html b/docs/reference/logLikelihood.html index f3c9f1f1..70c19ff2 100644 --- a/docs/reference/logLikelihood.html +++ b/docs/reference/logLikelihood.html @@ -73,7 +73,7 @@ celda - 1.11.0 + 1.12.0 diff --git a/docs/reference/logLikelihoodHistory.html b/docs/reference/logLikelihoodHistory.html index 1d83f9f3..f6fef915 100644 --- a/docs/reference/logLikelihoodHistory.html +++ b/docs/reference/logLikelihoodHistory.html @@ -73,7 +73,7 @@ celda - 1.11.0 + 1.12.0 diff --git a/docs/reference/matrixNames.html b/docs/reference/matrixNames.html index 30e2183d..ba77bcdf 100644 --- a/docs/reference/matrixNames.html +++ b/docs/reference/matrixNames.html @@ -73,7 +73,7 @@ celda - 1.11.0 + 1.12.0 diff --git a/docs/reference/moduleHeatmap.html b/docs/reference/moduleHeatmap.html index deda5cdc..2b4330ac 100644 --- a/docs/reference/moduleHeatmap.html +++ b/docs/reference/moduleHeatmap.html @@ -78,7 +78,7 @@ celda - 1.11.0 + 1.12.0 diff --git a/docs/reference/nonzero.html b/docs/reference/nonzero.html index 5e63ad5f..690947d3 100644 --- a/docs/reference/nonzero.html +++ b/docs/reference/nonzero.html @@ -72,7 +72,7 @@ celda - 1.11.0 + 1.12.0 diff --git a/docs/reference/normalizeCounts.html b/docs/reference/normalizeCounts.html index 0e6289d3..be4bcb126 100644 --- a/docs/reference/normalizeCounts.html +++ b/docs/reference/normalizeCounts.html @@ -73,7 +73,7 @@ celda - 1.11.0 + 1.12.0 diff --git a/docs/reference/params.html b/docs/reference/params.html index 9ce68c9a..5a19c90d 100644 --- a/docs/reference/params.html +++ b/docs/reference/params.html @@ -74,7 +74,7 @@ celda - 1.11.0 + 1.12.0 diff --git a/docs/reference/perplexity.html b/docs/reference/perplexity.html index 03a6ba7b..72ceb5aa 100644 --- a/docs/reference/perplexity.html +++ b/docs/reference/perplexity.html @@ -73,7 +73,7 @@ celda - 1.11.0 + 1.12.0 diff --git a/docs/reference/plotCeldaViolin.html b/docs/reference/plotCeldaViolin.html index 0b9f863a..bedce29f 100644 --- a/docs/reference/plotCeldaViolin.html +++ b/docs/reference/plotCeldaViolin.html @@ -72,7 +72,7 @@ celda - 1.11.0 + 1.12.0 diff --git a/docs/reference/plotDecontXContamination.html b/docs/reference/plotDecontXContamination.html index a5d04bb9..e7a0e6da 100644 --- a/docs/reference/plotDecontXContamination.html +++ b/docs/reference/plotDecontXContamination.html @@ -73,7 +73,7 @@ celda - 1.11.0 + 1.12.0 diff --git a/docs/reference/plotDecontXMarkerExpression.html b/docs/reference/plotDecontXMarkerExpression.html index 0d7e7169..5047a872 100644 --- a/docs/reference/plotDecontXMarkerExpression.html +++ b/docs/reference/plotDecontXMarkerExpression.html @@ -75,7 +75,7 @@ celda - 1.11.0 + 1.12.0 diff --git a/docs/reference/plotDecontXMarkerPercentage.html b/docs/reference/plotDecontXMarkerPercentage.html index 3d9c7ef1..3ef377b0 100644 --- a/docs/reference/plotDecontXMarkerPercentage.html +++ b/docs/reference/plotDecontXMarkerPercentage.html @@ -76,7 +76,7 @@ celda - 1.11.0 + 1.12.0 diff --git a/docs/reference/plotDimReduceCluster.html b/docs/reference/plotDimReduceCluster.html index 0033a741..f1741430 100644 --- a/docs/reference/plotDimReduceCluster.html +++ b/docs/reference/plotDimReduceCluster.html @@ -78,7 +78,7 @@ celda - 1.11.0 + 1.12.0 diff --git a/docs/reference/plotDimReduceFeature.html b/docs/reference/plotDimReduceFeature.html index 6bd34f1e..201392f6 100644 --- a/docs/reference/plotDimReduceFeature.html +++ b/docs/reference/plotDimReduceFeature.html @@ -75,7 +75,7 @@ celda - 1.11.0 + 1.12.0 diff --git a/docs/reference/plotDimReduceGrid.html b/docs/reference/plotDimReduceGrid.html index f4717ab3..2d6506e5 100644 --- a/docs/reference/plotDimReduceGrid.html +++ b/docs/reference/plotDimReduceGrid.html @@ -73,7 +73,7 @@ celda - 1.11.0 + 1.12.0 diff --git a/docs/reference/plotDimReduceModule.html b/docs/reference/plotDimReduceModule.html index ecdbf5a6..c023bca4 100644 --- a/docs/reference/plotDimReduceModule.html +++ b/docs/reference/plotDimReduceModule.html @@ -77,7 +77,7 @@ celda - 1.11.0 + 1.12.0 diff --git a/docs/reference/plotGridSearchPerplexity-1.png b/docs/reference/plotGridSearchPerplexity-1.png index 729dab98..f8212402 100644 Binary files a/docs/reference/plotGridSearchPerplexity-1.png and b/docs/reference/plotGridSearchPerplexity-1.png differ diff --git a/docs/reference/plotGridSearchPerplexity-2.png b/docs/reference/plotGridSearchPerplexity-2.png index 87cb6281..e3263a34 100644 Binary files a/docs/reference/plotGridSearchPerplexity-2.png and b/docs/reference/plotGridSearchPerplexity-2.png differ diff --git a/docs/reference/plotGridSearchPerplexity.html b/docs/reference/plotGridSearchPerplexity.html index 08974ce8..d8abd1b9 100644 --- a/docs/reference/plotGridSearchPerplexity.html +++ b/docs/reference/plotGridSearchPerplexity.html @@ -73,7 +73,7 @@ celda - 1.11.0 + 1.12.0 @@ -146,13 +146,13 @@

Visualize perplexity of a list of celda models

K/L combinations

- 
plotGridSearchPerplexity(x, altExpName = "featureSubset", sep = 1, alpha = 0.5)
+    
plotGridSearchPerplexity(x, altExpName = "featureSubset", sep = 5, alpha = 0.5)
 
 # S4 method for SingleCellExperiment
-plotGridSearchPerplexity(x, altExpName = "featureSubset", sep = 1, alpha = 0.5)
+plotGridSearchPerplexity(x, altExpName = "featureSubset", sep = 5, alpha = 0.5)
 
 # S4 method for celdaList
-plotGridSearchPerplexity(x, sep = 1, alpha = 0.5)

+plotGridSearchPerplexity(x, sep = 5, alpha = 0.5)

Arguments

diff --git a/docs/reference/plotHeatmap.html b/docs/reference/plotHeatmap.html index f958fcb2..3039db8d 100644 --- a/docs/reference/plotHeatmap.html +++ b/docs/reference/plotHeatmap.html @@ -73,7 +73,7 @@ celda - 1.11.0 + 1.12.0 diff --git a/docs/reference/plotRPC-1.png b/docs/reference/plotRPC-1.png index 63b58dea..0294be8b 100644 Binary files a/docs/reference/plotRPC-1.png and b/docs/reference/plotRPC-1.png differ diff --git a/docs/reference/plotRPC-2.png b/docs/reference/plotRPC-2.png index 08bf836a..dec44226 100644 Binary files a/docs/reference/plotRPC-2.png and b/docs/reference/plotRPC-2.png differ diff --git a/docs/reference/plotRPC.html b/docs/reference/plotRPC.html index dc4ce8f2..3446542d 100644 --- a/docs/reference/plotRPC.html +++ b/docs/reference/plotRPC.html @@ -41,8 +41,7 @@ + by unique K/L combinations." /> @@ -74,7 +73,7 @@ celda - 1.11.0 + 1.12.0 @@ -144,17 +143,16 @@

Visualize perplexity differences of a list of celda models

Visualize perplexity differences of every model in a celdaList, - by unique K/L combinations. Line represents centered moving average with - windows of length n.

+ by unique K/L combinations.

- 
plotRPC(x, altExpName = "featureSubset", sep = 1, n = 10, alpha = 0.5)
+    
plotRPC(x, altExpName = "featureSubset", sep = 5, alpha = 0.5)
 
 # S4 method for SingleCellExperiment
-plotRPC(x, altExpName = "featureSubset", sep = 1, n = 10, alpha = 0.5)
+plotRPC(x, altExpName = "featureSubset", sep = 5, alpha = 0.5)
 
 # S4 method for celdaList
-plotRPC(x, sep = 1, n = 10, alpha = 0.5)

+plotRPC(x, sep = 5, alpha = 0.5)

Arguments

@@ -178,10 +176,6 @@

Arg

- - - - - - - - - - - - @@ -390,36 +373,36 @@

Examp ## 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(sceCeldaCG, initialK = 3, maxK = 7) -
#> ==================================================
#> Starting recursive cell population splitting.
#> ==================================================
#> Thu Mar 31 11:11:32 2022 .. Initializing with 3 populations
#> Thu Mar 31 11:11:32 2022 .. Current cell population 4 | logLik: -1225755.01101897
#> Thu Mar 31 11:11:32 2022 .. Current cell population 5 | logLik: -1213677.60126784
#> Thu Mar 31 11:11:32 2022 .. Current cell population 6 | logLik: -1213903.59449854
#> Thu Mar 31 11:11:32 2022 .. Current cell population 7 | logLik: -1214081.54311397
#> Thu Mar 31 11:11:32 2022 .. Calculating perplexity
#> ==================================================
#> Completed recursive cell population splitting. Total time: 0.285394 secs
#> ==================================================
+
#> ==================================================
#> Starting recursive cell population splitting.
#> ==================================================
#> Sat Apr 30 15:15:13 2022 .. Initializing with 3 populations
#> Sat Apr 30 15:15:13 2022 .. Current cell population 4 | logLik: -1225755.01101897
#> Sat Apr 30 15:15:13 2022 .. Current cell population 5 | logLik: -1213677.60126784
#> Sat Apr 30 15:15:13 2022 .. Current cell population 6 | logLik: -1213903.59449854
#> Sat Apr 30 15:15:13 2022 .. Current cell population 7 | logLik: -1214081.54311397
#> Sat Apr 30 15:15:13 2022 .. Calculating perplexity
#> ==================================================
#> Completed recursive cell population splitting. Total time: 0.2865281 secs
#> ==================================================
## Alternatively, first identify features modules using ## \link{recursiveSplitModule} moduleSplit <- recursiveSplitModule(sceCeldaCG, initialL = 3, maxL = 15) -
#> ==================================================
#> Starting recursive module splitting.
#> ==================================================
#> Thu Mar 31 11:11:32 2022 .. Collapsing to 100 temporary cell populations
#> Thu Mar 31 11:11:33 2022 .. Initializing with 3 modules
#> Thu Mar 31 11:11:33 2022 .. Created module 4 | logLik: -1241379.90928455
#> Thu Mar 31 11:11:33 2022 .. Created module 5 | logLik: -1235212.7977535
#> Thu Mar 31 11:11:34 2022 .. Created module 6 | logLik: -1232789.9817561
#> Thu Mar 31 11:11:34 2022 .. Created module 7 | logLik: -1227246.66090571
#> Thu Mar 31 11:11:34 2022 .. Created module 8 | logLik: -1223898.757694
#> Thu Mar 31 11:11:34 2022 .. Created module 9 | logLik: -1221848.26936098
#> Thu Mar 31 11:11:34 2022 .. Created module 10 | logLik: -1220147.96681948
#> Thu Mar 31 11:11:34 2022 .. Created module 11 | logLik: -1220818.37022325
#> Thu Mar 31 11:11:34 2022 .. Created module 12 | logLik: -1221489.07685946
#> Thu Mar 31 11:11:34 2022 .. Created module 13 | logLik: -1222032.53497571
#> Thu Mar 31 11:11:34 2022 .. Created module 14 | logLik: -1222712.17543857
#> Thu Mar 31 11:11:34 2022 .. Created module 15 | logLik: -1223268.97596756
#> Thu Mar 31 11:11:34 2022 .. Calculating perplexity
#> ==================================================
#> Completed recursive module splitting. Total time: 2.224735 secs
#> ==================================================
plotGridSearchPerplexity(moduleSplit) +
#> ==================================================
#> Starting recursive module splitting.
#> ==================================================
#> Sat Apr 30 15:15:13 2022 .. Collapsing to 100 temporary cell populations
#> Sat Apr 30 15:15:14 2022 .. Initializing with 3 modules
#> Sat Apr 30 15:15:14 2022 .. Created module 4 | logLik: -1241379.90928455
#> Sat Apr 30 15:15:14 2022 .. Created module 5 | logLik: -1235212.7977535
#> Sat Apr 30 15:15:14 2022 .. Created module 6 | logLik: -1232789.9817561
#> Sat Apr 30 15:15:14 2022 .. Created module 7 | logLik: -1227246.66090571
#> Sat Apr 30 15:15:14 2022 .. Created module 8 | logLik: -1223898.757694
#> Sat Apr 30 15:15:14 2022 .. Created module 9 | logLik: -1221848.26936098
#> Sat Apr 30 15:15:15 2022 .. Created module 10 | logLik: -1220147.96681948
#> Sat Apr 30 15:15:15 2022 .. Created module 11 | logLik: -1220818.37022325
#> Sat Apr 30 15:15:15 2022 .. Created module 12 | logLik: -1221489.07685946
#> Sat Apr 30 15:15:15 2022 .. Created module 13 | logLik: -1222032.53497571
#> Sat Apr 30 15:15:15 2022 .. Created module 14 | logLik: -1222712.17543857
#> Sat Apr 30 15:15:15 2022 .. Created module 15 | logLik: -1223268.97596756
#> Sat Apr 30 15:15:15 2022 .. Calculating perplexity
#> ==================================================
#> Completed recursive module splitting. Total time: 2.031379 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.
#> ==================================================
#> Thu Mar 31 11:11:35 2022 .. Collapsing to 10 modules
#> Thu Mar 31 11:11:35 2022 .. Initializing with 3 populations
#> Thu Mar 31 11:11:35 2022 .. Current cell population 4 | logLik: -1225286.49558716
#> Thu Mar 31 11:11:35 2022 .. Current cell population 5 | logLik: -1212955.15575681
#> Thu Mar 31 11:11:36 2022 .. Current cell population 6 | logLik: -1212982.74290613
#> Thu Mar 31 11:11:36 2022 .. Current cell population 7 | logLik: -1213005.40337891
#> Thu Mar 31 11:11:36 2022 .. Calculating perplexity
#> ==================================================
#> Completed recursive cell population splitting. Total time: 1.023948 secs
#> ==================================================
plotGridSearchPerplexity(cellSplit) +
#> ==================================================
#> Starting recursive cell population splitting.
#> ==================================================
#> Sat Apr 30 15:15:15 2022 .. Collapsing to 10 modules
#> Sat Apr 30 15:15:15 2022 .. Initializing with 3 populations
#> Sat Apr 30 15:15:16 2022 .. Current cell population 4 | logLik: -1225286.49558716
#> Sat Apr 30 15:15:16 2022 .. Current cell population 5 | logLik: -1212955.15575681
#> Sat Apr 30 15:15:16 2022 .. Current cell population 6 | logLik: -1212982.74290613
#> Sat Apr 30 15:15:16 2022 .. Current cell population 7 | logLik: -1213005.40337891
#> Sat Apr 30 15:15:16 2022 .. Calculating perplexity
#> ==================================================
#> Completed recursive cell population splitting. Total time: 0.936219 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$counts, initialK = 3, maxK = 7) -
#> ==================================================
#> Starting recursive cell population splitting.
#> ==================================================
#> Thu Mar 31 11:11:36 2022 .. Initializing with 3 populations
#> Thu Mar 31 11:11:36 2022 .. Current cell population 4 | logLik: -1341630.1679001
#> Thu Mar 31 11:11:36 2022 .. Current cell population 5 | logLik: -1327506.91718317
#> Thu Mar 31 11:11:36 2022 .. Current cell population 6 | logLik: -1315227.54586167
#> Thu Mar 31 11:11:36 2022 .. Current cell population 7 | logLik: -1304393.65802293
#> Thu Mar 31 11:11:36 2022 .. Calculating perplexity
#> ==================================================
#> Completed recursive cell population splitting. Total time: 0.2181861 secs
#> ==================================================
+
#> ==================================================
#> Starting recursive cell population splitting.
#> ==================================================
#> Sat Apr 30 15:15:17 2022 .. Initializing with 3 populations
#> Sat Apr 30 15:15:17 2022 .. Current cell population 4 | logLik: -1341630.1679001
#> Sat Apr 30 15:15:17 2022 .. Current cell population 5 | logLik: -1327506.91718317
#> Sat Apr 30 15:15:17 2022 .. Current cell population 6 | logLik: -1315227.54586167
#> Sat Apr 30 15:15:17 2022 .. Current cell population 7 | logLik: -1304393.65802293
#> Sat Apr 30 15:15:17 2022 .. Calculating perplexity
#> ==================================================
#> Completed recursive cell population splitting. Total time: 0.2249022 secs
#> ==================================================
## Alternatively, first identify features modules using ## \link{recursiveSplitModule} moduleSplit <- recursiveSplitModule(celdaCGSim$counts, initialL = 3, maxL = 15) -
#> ==================================================
#> Starting recursive module splitting.
#> ==================================================
#> Thu Mar 31 11:11:36 2022 .. Collapsing to 100 temporary cell populations
#> Thu Mar 31 11:11:37 2022 .. Initializing with 3 modules
#> Thu Mar 31 11:11:38 2022 .. Created module 4 | logLik: -1243396.62348886
#> Thu Mar 31 11:11:38 2022 .. Created module 5 | logLik: -1237610.11790137
#> Thu Mar 31 11:11:38 2022 .. Created module 6 | logLik: -1232128.87013396
#> Thu Mar 31 11:11:38 2022 .. Created module 7 | logLik: -1227611.8250329
#> Thu Mar 31 11:11:38 2022 .. Created module 8 | logLik: -1225618.06184004
#> Thu Mar 31 11:11:38 2022 .. Created module 9 | logLik: -1223967.77531912
#> Thu Mar 31 11:11:38 2022 .. Created module 10 | logLik: -1222801.11395987
#> Thu Mar 31 11:11:38 2022 .. Created module 11 | logLik: -1223402.66903597
#> Thu Mar 31 11:11:38 2022 .. Created module 12 | logLik: -1224026.19892208
#> Thu Mar 31 11:11:38 2022 .. Created module 13 | logLik: -1224675.63005464
#> Thu Mar 31 11:11:38 2022 .. Created module 14 | logLik: -1225317.91966369
#> Thu Mar 31 11:11:39 2022 .. Created module 15 | logLik: -1225971.50555157
#> Thu Mar 31 11:11:39 2022 .. Calculating perplexity
#> ==================================================
#> Completed recursive module splitting. Total time: 2.145409 secs
#> ==================================================
plotGridSearchPerplexity(moduleSplit) +
#> ==================================================
#> Starting recursive module splitting.
#> ==================================================
#> Sat Apr 30 15:15:17 2022 .. Collapsing to 100 temporary cell populations
#> Sat Apr 30 15:15:18 2022 .. Initializing with 3 modules
#> Sat Apr 30 15:15:18 2022 .. Created module 4 | logLik: -1243396.62348886
#> Sat Apr 30 15:15:18 2022 .. Created module 5 | logLik: -1237610.11790137
#> Sat Apr 30 15:15:18 2022 .. Created module 6 | logLik: -1232128.87013396
#> Sat Apr 30 15:15:18 2022 .. Created module 7 | logLik: -1227611.8250329
#> Sat Apr 30 15:15:18 2022 .. Created module 8 | logLik: -1225618.06184004
#> Sat Apr 30 15:15:18 2022 .. Created module 9 | logLik: -1223967.77531912
#> Sat Apr 30 15:15:18 2022 .. Created module 10 | logLik: -1222801.11395987
#> Sat Apr 30 15:15:18 2022 .. Created module 11 | logLik: -1223402.66903597
#> Sat Apr 30 15:15:19 2022 .. Created module 12 | logLik: -1224026.19892208
#> Sat Apr 30 15:15:19 2022 .. Created module 13 | logLik: -1224675.63005464
#> Sat Apr 30 15:15:19 2022 .. Created module 14 | logLik: -1225317.91966369
#> Sat Apr 30 15:15:19 2022 .. Created module 15 | logLik: -1225971.50555157
#> Sat Apr 30 15:15:19 2022 .. Calculating perplexity
#> ==================================================
#> Completed recursive module splitting. Total time: 2.012394 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.
#> ==================================================
#> Thu Mar 31 11:11:39 2022 .. Collapsing to 10 modules
#> Thu Mar 31 11:11:39 2022 .. Initializing with 3 populations
#> Thu Mar 31 11:11:41 2022 .. Current cell population 4 | logLik: -1227944.5458832
#> Thu Mar 31 11:11:41 2022 .. Current cell population 5 | logLik: -1215605.08613503
#> Thu Mar 31 11:11:41 2022 .. Current cell population 6 | logLik: -1215627.62281773
#> Thu Mar 31 11:11:41 2022 .. Current cell population 7 | logLik: -1215651.32538066
#> Thu Mar 31 11:11:41 2022 .. Calculating perplexity
#> ==================================================
#> Completed recursive cell population splitting. Total time: 2.215127 secs
#> ==================================================
plotGridSearchPerplexity(cellSplit) +
#> ==================================================
#> Starting recursive cell population splitting.
#> ==================================================
#> Sat Apr 30 15:15:19 2022 .. Collapsing to 10 modules
#> Sat Apr 30 15:15:19 2022 .. Initializing with 3 populations
#> Sat Apr 30 15:15:21 2022 .. Current cell population 4 | logLik: -1227944.5458832
#> Sat Apr 30 15:15:21 2022 .. Current cell population 5 | logLik: -1215605.08613503
#> Sat Apr 30 15:15:21 2022 .. Current cell population 6 | logLik: -1215627.62281773
#> Sat Apr 30 15:15:21 2022 .. Current cell population 7 | logLik: -1215651.32538066
#> Sat Apr 30 15:15:21 2022 .. Calculating perplexity
#> ==================================================
#> Completed recursive cell population splitting. Total time: 1.633234 secs
#> ==================================================
plotGridSearchPerplexity(cellSplit)
sce <- subsetCeldaList(cellSplit, list(K = 5, L = 10))
diff --git a/docs/reference/recursiveSplitModule-1.png b/docs/reference/recursiveSplitModule-1.png index 626a0f1c..0e02b65f 100644 Binary files a/docs/reference/recursiveSplitModule-1.png and b/docs/reference/recursiveSplitModule-1.png differ diff --git a/docs/reference/recursiveSplitModule-2.png b/docs/reference/recursiveSplitModule-2.png index cde1e980..47e5019e 100644 Binary files a/docs/reference/recursiveSplitModule-2.png and b/docs/reference/recursiveSplitModule-2.png differ diff --git a/docs/reference/recursiveSplitModule.html b/docs/reference/recursiveSplitModule.html index 9bae32d6..c53db89e 100644 --- a/docs/reference/recursiveSplitModule.html +++ b/docs/reference/recursiveSplitModule.html @@ -77,7 +77,7 @@ celda - 1.11.0 + 1.12.0 @@ -172,9 +172,7 @@

Recursive module splitting

seed =12345, perplexity =TRUE, doResampling =FALSE, - doSubsampling =TRUE, numResample =5, - numSubsample =5000, verbose =TRUE, logfile =NULL) @@ -198,9 +196,7 @@

Recursive module splitting

seed =12345, perplexity =TRUE, doResampling =FALSE, - doSubsampling =TRUE, numResample =5, - numSubsample =5000, verbose =TRUE, logfile =NULL) @@ -224,9 +220,7 @@

Recursive module splitting

seed =12345, perplexity =TRUE, doResampling =FALSE, - doSubsampling =TRUE, numResample =5, - numSubsample =5000, verbose =TRUE, logfile =NULL) @@ -331,23 +325,12 @@

Arg

- - - - - - - - @@ -377,7 +360,7 @@

Examp ## Create models that range from L=3 to L=20 by recursively splitting modules ## into two moduleSplit <- recursiveSplitModule(sceCeldaCG, initialL = 3, maxL = 20) -
#> ==================================================
#> Starting recursive module splitting.
#> ==================================================
#> Thu Mar 31 11:11:42 2022 .. Collapsing to 100 temporary cell populations
#> Thu Mar 31 11:11:44 2022 .. Initializing with 3 modules
#> Thu Mar 31 11:11:44 2022 .. Created module 4 | logLik: -1241379.90928455
#> Thu Mar 31 11:11:44 2022 .. Created module 5 | logLik: -1235212.7977535
#> Thu Mar 31 11:11:44 2022 .. Created module 6 | logLik: -1232789.9817561
#> Thu Mar 31 11:11:44 2022 .. Created module 7 | logLik: -1227246.66090571
#> Thu Mar 31 11:11:44 2022 .. Created module 8 | logLik: -1223898.757694
#> Thu Mar 31 11:11:44 2022 .. Created module 9 | logLik: -1221848.26936098
#> Thu Mar 31 11:11:44 2022 .. Created module 10 | logLik: -1220147.96681948
#> Thu Mar 31 11:11:44 2022 .. Created module 11 | logLik: -1220818.37022325
#> Thu Mar 31 11:11:44 2022 .. Created module 12 | logLik: -1221489.07685946
#> Thu Mar 31 11:11:45 2022 .. Created module 13 | logLik: -1222032.53497571
#> Thu Mar 31 11:11:45 2022 .. Created module 14 | logLik: -1222712.17543857
#> Thu Mar 31 11:11:45 2022 .. Created module 15 | logLik: -1223268.97596756
#> Thu Mar 31 11:11:45 2022 .. Created module 16 | logLik: -1223841.4834406
#> Thu Mar 31 11:11:45 2022 .. Created module 17 | logLik: -1224394.02513994
#> Thu Mar 31 11:11:45 2022 .. Created module 18 | logLik: -1224863.41435811
#> Thu Mar 31 11:11:45 2022 .. Created module 19 | logLik: -1225480.30453125
#> Thu Mar 31 11:11:45 2022 .. Created module 20 | logLik: -1226156.47078695
#> Thu Mar 31 11:11:45 2022 .. Calculating perplexity
#> ==================================================
#> Completed recursive module splitting. Total time: 2.905554 secs
#> ==================================================
+
#> ==================================================
#> Starting recursive module splitting.
#> ==================================================
#> Sat Apr 30 15:15:22 2022 .. Collapsing to 100 temporary cell populations
#> Sat Apr 30 15:15:23 2022 .. Initializing with 3 modules
#> Sat Apr 30 15:15:23 2022 .. Created module 4 | logLik: -1241379.90928455
#> Sat Apr 30 15:15:23 2022 .. Created module 5 | logLik: -1235212.7977535
#> Sat Apr 30 15:15:23 2022 .. Created module 6 | logLik: -1232789.9817561
#> Sat Apr 30 15:15:24 2022 .. Created module 7 | logLik: -1227246.66090571
#> Sat Apr 30 15:15:24 2022 .. Created module 8 | logLik: -1223898.757694
#> Sat Apr 30 15:15:24 2022 .. Created module 9 | logLik: -1221848.26936098
#> Sat Apr 30 15:15:24 2022 .. Created module 10 | logLik: -1220147.96681948
#> Sat Apr 30 15:15:24 2022 .. Created module 11 | logLik: -1220818.37022325
#> Sat Apr 30 15:15:24 2022 .. Created module 12 | logLik: -1221489.07685946
#> Sat Apr 30 15:15:24 2022 .. Created module 13 | logLik: -1222032.53497571
#> Sat Apr 30 15:15:24 2022 .. Created module 14 | logLik: -1222712.17543857
#> Sat Apr 30 15:15:24 2022 .. Created module 15 | logLik: -1223268.97596756
#> Sat Apr 30 15:15:24 2022 .. Created module 16 | logLik: -1223841.4834406
#> Sat Apr 30 15:15:24 2022 .. Created module 17 | logLik: -1224394.02513994
#> Sat Apr 30 15:15:25 2022 .. Created module 18 | logLik: -1224863.41435811
#> Sat Apr 30 15:15:25 2022 .. Created module 19 | logLik: -1225480.30453125
#> Sat Apr 30 15:15:25 2022 .. Created module 20 | logLik: -1226156.47078695
#> Sat Apr 30 15:15:25 2022 .. Calculating perplexity
#> ==================================================
#> Completed recursive module splitting. Total time: 2.877337 secs
#> ==================================================
## Example results with perplexity plotGridSearchPerplexity(moduleSplit)
@@ -388,7 +371,7 @@

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

#> ==================================================
#> Starting recursive module splitting.
#> ==================================================
#> Thu Mar 31 11:11:46 2022 .. Collapsing to 100 temporary cell populations
#> Thu Mar 31 11:11:46 2022 .. Initializing with 3 modules
#> Thu Mar 31 11:11:47 2022 .. Created module 4 | logLik: -1243396.62348886
#> Thu Mar 31 11:11:47 2022 .. Created module 5 | logLik: -1237610.11790137
#> Thu Mar 31 11:11:47 2022 .. Created module 6 | logLik: -1232128.87013396
#> Thu Mar 31 11:11:47 2022 .. Created module 7 | logLik: -1227611.8250329
#> Thu Mar 31 11:11:47 2022 .. Created module 8 | logLik: -1225618.06184004
#> Thu Mar 31 11:11:47 2022 .. Created module 9 | logLik: -1223967.77531912
#> Thu Mar 31 11:11:47 2022 .. Created module 10 | logLik: -1222801.11395987
#> Thu Mar 31 11:11:47 2022 .. Created module 11 | logLik: -1223402.66903597
#> Thu Mar 31 11:11:47 2022 .. Created module 12 | logLik: -1224026.19892208
#> Thu Mar 31 11:11:47 2022 .. Created module 13 | logLik: -1224675.63005464
#> Thu Mar 31 11:11:47 2022 .. Created module 14 | logLik: -1225317.91966369
#> Thu Mar 31 11:11:47 2022 .. Created module 15 | logLik: -1225971.50555157
#> Thu Mar 31 11:11:48 2022 .. Created module 16 | logLik: -1226557.7881506
#> Thu Mar 31 11:11:48 2022 .. Created module 17 | logLik: -1227080.13473523
#> Thu Mar 31 11:11:48 2022 .. Created module 18 | logLik: -1227603.99622355
#> Thu Mar 31 11:11:48 2022 .. Created module 19 | logLik: -1228247.84169741
#> Thu Mar 31 11:11:48 2022 .. Created module 20 | logLik: -1228828.70617002
#> Thu Mar 31 11:11:48 2022 .. Calculating perplexity
#> ==================================================
#> Completed recursive module splitting. Total time: 2.42274 secs
#> ==================================================
+
#> ==================================================
#> Starting recursive module splitting.
#> ==================================================
#> Sat Apr 30 15:15:25 2022 .. Collapsing to 100 temporary cell populations
#> Sat Apr 30 15:15:26 2022 .. Initializing with 3 modules
#> Sat Apr 30 15:15:26 2022 .. Created module 4 | logLik: -1243396.62348886
#> Sat Apr 30 15:15:26 2022 .. Created module 5 | logLik: -1237610.11790137
#> Sat Apr 30 15:15:26 2022 .. Created module 6 | logLik: -1232128.87013396
#> Sat Apr 30 15:15:26 2022 .. Created module 7 | logLik: -1227611.8250329
#> Sat Apr 30 15:15:26 2022 .. Created module 8 | logLik: -1225618.06184004
#> Sat Apr 30 15:15:26 2022 .. Created module 9 | logLik: -1223967.77531912
#> Sat Apr 30 15:15:26 2022 .. Created module 10 | logLik: -1222801.11395987
#> Sat Apr 30 15:15:27 2022 .. Created module 11 | logLik: -1223402.66903597
#> Sat Apr 30 15:15:27 2022 .. Created module 12 | logLik: -1224026.19892208
#> Sat Apr 30 15:15:27 2022 .. Created module 13 | logLik: -1224675.63005464
#> Sat Apr 30 15:15:27 2022 .. Created module 14 | logLik: -1225317.91966369
#> Sat Apr 30 15:15:27 2022 .. Created module 15 | logLik: -1225971.50555157
#> Sat Apr 30 15:15:27 2022 .. Created module 16 | logLik: -1226557.7881506
#> Sat Apr 30 15:15:27 2022 .. Created module 17 | logLik: -1227080.13473523
#> Sat Apr 30 15:15:27 2022 .. Created module 18 | logLik: -1227603.99622355
#> Sat Apr 30 15:15:27 2022 .. Created module 19 | logLik: -1228247.84169741
#> Sat Apr 30 15:15:27 2022 .. Created module 20 | logLik: -1228828.70617002
#> Sat Apr 30 15:15:27 2022 .. Calculating perplexity
#> ==================================================
#> Completed recursive module splitting. Total time: 2.221109 secs
#> ==================================================
## Example results with perplexity plotGridSearchPerplexity(moduleSplit)
diff --git a/docs/reference/reorderCelda.html b/docs/reference/reorderCelda.html index ab641c40..19774c2b 100644 --- a/docs/reference/reorderCelda.html +++ b/docs/reference/reorderCelda.html @@ -77,7 +77,7 @@ celda - 1.11.0 + 1.12.0
diff --git a/docs/reference/reportceldaCG.html b/docs/reference/reportceldaCG.html index a2a93f72..2f25b791 100644 --- a/docs/reference/reportceldaCG.html +++ b/docs/reference/reportceldaCG.html @@ -79,7 +79,7 @@ celda - 1.11.0 + 1.12.0 diff --git a/docs/reference/resList.html b/docs/reference/resList.html index 421fe16b..83f4c9ba 100644 --- a/docs/reference/resList.html +++ b/docs/reference/resList.html @@ -75,7 +75,7 @@ celda - 1.11.0 + 1.12.0 diff --git a/docs/reference/resamplePerplexity-1.png b/docs/reference/resamplePerplexity-1.png index 87600492..31f7d770 100644 Binary files a/docs/reference/resamplePerplexity-1.png and b/docs/reference/resamplePerplexity-1.png differ diff --git a/docs/reference/resamplePerplexity-2.png b/docs/reference/resamplePerplexity-2.png index 3d51b965..6b596757 100644 Binary files a/docs/reference/resamplePerplexity-2.png and b/docs/reference/resamplePerplexity-2.png differ diff --git a/docs/reference/resamplePerplexity.html b/docs/reference/resamplePerplexity.html index c602e248..9b870843 100644 --- a/docs/reference/resamplePerplexity.html +++ b/docs/reference/resamplePerplexity.html @@ -75,7 +75,7 @@ celda - 1.11.0 + 1.12.0 @@ -156,9 +156,7 @@

Calculate and visualize perplexity of all models in a celdaList

useAssay ="counts", altExpName ="featureSubset", doResampling =FALSE, - doSubsampling =TRUE, numResample =5, - numSubsample =5000, seed =12345) @@ -168,9 +166,7 @@

Calculate and visualize perplexity of all models in a celdaList

useAssay ="counts", altExpName ="featureSubset", doResampling =FALSE, - doSubsampling =TRUE, numResample =5, - numSubsample =5000, seed =12345) @@ -179,9 +175,7 @@

Calculate and visualize perplexity of all models in a celdaList

x, celdaList, doResampling =FALSE, - doSubsampling =TRUE, numResample =5, - numSubsample =5000, seed =12345) @@ -218,23 +212,12 @@

Arg

- - - - - - - - diff --git a/docs/reference/retrieveFeatureIndex.html b/docs/reference/retrieveFeatureIndex.html index 96e55334..825532df 100644 --- a/docs/reference/retrieveFeatureIndex.html +++ b/docs/reference/retrieveFeatureIndex.html @@ -76,7 +76,7 @@ celda - 1.11.0 + 1.12.0 diff --git a/docs/reference/runParams.html b/docs/reference/runParams.html index b1a5471f..1a97c35f 100644 --- a/docs/reference/runParams.html +++ b/docs/reference/runParams.html @@ -75,7 +75,7 @@ celda - 1.11.0 + 1.12.0 diff --git a/docs/reference/sampleCells.html b/docs/reference/sampleCells.html index 9d80141b..aa7194f4 100644 --- a/docs/reference/sampleCells.html +++ b/docs/reference/sampleCells.html @@ -72,7 +72,7 @@ celda - 1.11.0 + 1.12.0 diff --git a/docs/reference/sampleLabel.html b/docs/reference/sampleLabel.html index c68f0c9f..3da498b3 100644 --- a/docs/reference/sampleLabel.html +++ b/docs/reference/sampleLabel.html @@ -74,7 +74,7 @@ celda - 1.11.0 + 1.12.0 diff --git a/docs/reference/sceCeldaC.html b/docs/reference/sceCeldaC.html index 1260a15d..ccbe1028 100644 --- a/docs/reference/sceCeldaC.html +++ b/docs/reference/sceCeldaC.html @@ -74,7 +74,7 @@ celda - 1.11.0 + 1.12.0 @@ -162,7 +162,7 @@

Examp K = celdaCSim$K, sampleLabel = celdaCSim$sampleLabel, nchains = 1) -
#> --------------------------------------------------
#> Starting Celda_C: Clustering cells.
#> --------------------------------------------------
#> Thu Mar 31 11:11:52 2022 .. Initializing 'z' in chain 1 with 'split'
#> Thu Mar 31 11:11:52 2022 .... Completed iteration: 1 | logLik: -1282027.27277705
#> Thu Mar 31 11:11:52 2022 .... Completed iteration: 2 | logLik: -1282027.27277705
#> Thu Mar 31 11:11:52 2022 .. Finished chain 1
#> --------------------------------------------------
#> Completed Celda_C. Total time: 0.06023312 secs
#> --------------------------------------------------
+
#> --------------------------------------------------
#> Starting Celda_C: Clustering cells.
#> --------------------------------------------------
#> Sat Apr 30 15:15:31 2022 .. Initializing 'z' in chain 1 with 'split'
#> Sat Apr 30 15:15:31 2022 .... Completed iteration: 1 | logLik: -1282027.27277705
#> Sat Apr 30 15:15:31 2022 .... Completed iteration: 2 | logLik: -1282027.27277705
#> Sat Apr 30 15:15:31 2022 .. Finished chain 1
#> --------------------------------------------------
#> Completed Celda_C. Total time: 0.05844092 secs
#> --------------------------------------------------
@@ -163,7 +163,7 @@

Examp L = celdaCGSim$L, sampleLabel = celdaCGSim$sampleLabel, nchains = 1) -
#> --------------------------------------------------
#> Starting Celda_CG: Clustering cells and genes.
#> --------------------------------------------------
#> Thu Mar 31 11:11:52 2022 .. Initializing 'z' in chain 1 with 'split'
#> Thu Mar 31 11:11:52 2022 .. Initializing 'y' in chain 1 with 'split'
#> Thu Mar 31 11:11:54 2022 .... Completed iteration: 1 | logLik: -1212891.16546068
#> Thu Mar 31 11:11:54 2022 .... Completed iteration: 2 | logLik: -1212891.16546068
#> Thu Mar 31 11:11:54 2022 .... Completed iteration: 3 | logLik: -1212891.16546068
#> Thu Mar 31 11:11:54 2022 .... Completed iteration: 4 | logLik: -1212891.16546068
#> Thu Mar 31 11:11:54 2022 .... Completed iteration: 5 | logLik: -1212891.16546068
#> Thu Mar 31 11:11:54 2022 .... Completed iteration: 6 | logLik: -1212891.16546068
#> Thu Mar 31 11:11:54 2022 .... Completed iteration: 7 | logLik: -1212891.16546068
#> Thu Mar 31 11:11:54 2022 .... Completed iteration: 8 | logLik: -1212891.16546068
#> Thu Mar 31 11:11:54 2022 .... Completed iteration: 9 | logLik: -1212891.16546068
#> Thu Mar 31 11:11:54 2022 .... Determining if any gene clusters should be split.
#> Thu Mar 31 11:11:54 2022 .... No additional splitting was performed.
#> Thu Mar 31 11:11:54 2022 .... Determining if any cell clusters should be split.
#> Thu Mar 31 11:11:54 2022 .... No additional splitting was performed.
#> Thu Mar 31 11:11:54 2022 .... Completed iteration: 10 | logLik: -1212891.16546068
#> Thu Mar 31 11:11:54 2022 .... Determining if any cell clusters should be split.
#> Thu Mar 31 11:11:54 2022 .... No additional splitting was performed.
#> Thu Mar 31 11:11:54 2022 .... Completed iteration: 11 | logLik: -1212891.16546068
#> Thu Mar 31 11:11:54 2022 .. Finished chain 1
#> --------------------------------------------------
#> Completed Celda_CG. Total time: 2.526008 secs
#> --------------------------------------------------
+
#> --------------------------------------------------
#> Starting Celda_CG: Clustering cells and genes.
#> --------------------------------------------------
#> Sat Apr 30 15:15:31 2022 .. Initializing 'z' in chain 1 with 'split'
#> Sat Apr 30 15:15:31 2022 .. Initializing 'y' in chain 1 with 'split'
#> Sat Apr 30 15:15:33 2022 .... Completed iteration: 1 | logLik: -1212891.16546068
#> Sat Apr 30 15:15:33 2022 .... Completed iteration: 2 | logLik: -1212891.16546068
#> Sat Apr 30 15:15:33 2022 .... Completed iteration: 3 | logLik: -1212891.16546068
#> Sat Apr 30 15:15:33 2022 .... Completed iteration: 4 | logLik: -1212891.16546068
#> Sat Apr 30 15:15:33 2022 .... Completed iteration: 5 | logLik: -1212891.16546068
#> Sat Apr 30 15:15:33 2022 .... Completed iteration: 6 | logLik: -1212891.16546068
#> Sat Apr 30 15:15:33 2022 .... Completed iteration: 7 | logLik: -1212891.16546068
#> Sat Apr 30 15:15:33 2022 .... Completed iteration: 8 | logLik: -1212891.16546068
#> Sat Apr 30 15:15:33 2022 .... Completed iteration: 9 | logLik: -1212891.16546068
#> Sat Apr 30 15:15:33 2022 .... Determining if any gene clusters should be split.
#> Sat Apr 30 15:15:33 2022 .... No additional splitting was performed.
#> Sat Apr 30 15:15:33 2022 .... Determining if any cell clusters should be split.
#> Sat Apr 30 15:15:33 2022 .... No additional splitting was performed.
#> Sat Apr 30 15:15:33 2022 .... Completed iteration: 10 | logLik: -1212891.16546068
#> Sat Apr 30 15:15:33 2022 .... Determining if any cell clusters should be split.
#> Sat Apr 30 15:15:33 2022 .... No additional splitting was performed.
#> Sat Apr 30 15:15:33 2022 .... Completed iteration: 11 | logLik: -1212891.16546068
#> Sat Apr 30 15:15:33 2022 .. Finished chain 1
#> --------------------------------------------------
#> Completed Celda_CG. Total time: 2.366771 secs
#> --------------------------------------------------
diff --git a/docs/reference/sceCeldaG.html b/docs/reference/sceCeldaG.html index 7e76f77d..0350a201 100644 --- a/docs/reference/sceCeldaG.html +++ b/docs/reference/sceCeldaG.html @@ -74,7 +74,7 @@ celda - 1.11.0 + 1.12.0 @@ -159,7 +159,7 @@

Examp 
data(celdaGSim)
 sceCeldaG <- selectFeatures(celdaGSim$counts)
 sceCeldaG <- celda_G(sceCeldaG, L = celdaGSim$L, nchains = 1)
-
#> --------------------------------------------------
#> Starting Celda_G: Clustering genes.
#> --------------------------------------------------
#> Thu Mar 31 11:12:27 2022 .. Initializing 'y' in chain 1 with 'split' 
#> Thu Mar 31 11:12:27 2022 .... Completed iteration: 1 | logLik: -289209.476865707
#> Thu Mar 31 11:12:27 2022 .... Completed iteration: 2 | logLik: -289209.476865707
#> Thu Mar 31 11:12:27 2022 .... Completed iteration: 3 | logLik: -289209.476865707
#> Thu Mar 31 11:12:27 2022 .... Completed iteration: 4 | logLik: -289209.476865707
#> Thu Mar 31 11:12:27 2022 .... Completed iteration: 5 | logLik: -289209.476865707
#> Thu Mar 31 11:12:27 2022 .... Completed iteration: 6 | logLik: -289209.476865707
#> Thu Mar 31 11:12:27 2022 .... Completed iteration: 7 | logLik: -289209.476865707
#> Thu Mar 31 11:12:27 2022 .... Completed iteration: 8 | logLik: -289209.476865707
#> Thu Mar 31 11:12:27 2022 .... Completed iteration: 9 | logLik: -289209.476865707
#> Thu Mar 31 11:12:27 2022 .... Determining if any gene clusters should be split.
#> Thu Mar 31 11:12:27 2022 .... No additional splitting was performed.
#> Thu Mar 31 11:12:27 2022 .... Completed iteration: 10 | logLik: -289209.476865707
#> Thu Mar 31 11:12:27 2022 .... Completed iteration: 11 | logLik: -289209.476865707
#> Thu Mar 31 11:12:27 2022 .. Finished chain 1
#> --------------------------------------------------
#> Completed Celda_G. Total time: 0.302249 secs
#> --------------------------------------------------
+
#> --------------------------------------------------
#> Starting Celda_G: Clustering genes.
#> --------------------------------------------------
#> Sat Apr 30 15:16:03 2022 .. Initializing 'y' in chain 1 with 'split'
#> Sat Apr 30 15:16:03 2022 .... Completed iteration: 1 | logLik: -289209.476865707
#> Sat Apr 30 15:16:03 2022 .... Completed iteration: 2 | logLik: -289209.476865707
#> Sat Apr 30 15:16:03 2022 .... Completed iteration: 3 | logLik: -289209.476865707
#> Sat Apr 30 15:16:03 2022 .... Completed iteration: 4 | logLik: -289209.476865707
#> Sat Apr 30 15:16:03 2022 .... Completed iteration: 5 | logLik: -289209.476865707
#> Sat Apr 30 15:16:03 2022 .... Completed iteration: 6 | logLik: -289209.476865707
#> Sat Apr 30 15:16:03 2022 .... Completed iteration: 7 | logLik: -289209.476865707
#> Sat Apr 30 15:16:03 2022 .... Completed iteration: 8 | logLik: -289209.476865707
#> Sat Apr 30 15:16:03 2022 .... Completed iteration: 9 | logLik: -289209.476865707
#> Sat Apr 30 15:16:03 2022 .... Determining if any gene clusters should be split.
#> Sat Apr 30 15:16:03 2022 .... No additional splitting was performed.
#> Sat Apr 30 15:16:03 2022 .... Completed iteration: 10 | logLik: -289209.476865707
#> Sat Apr 30 15:16:03 2022 .... Completed iteration: 11 | logLik: -289209.476865707
#> Sat Apr 30 15:16:03 2022 .. Finished chain 1
#> --------------------------------------------------
#> Completed Celda_G. Total time: 0.313231 secs
#> --------------------------------------------------
diff --git a/docs/reference/selectFeatures.html b/docs/reference/selectFeatures.html index 42b96c4d..e8f12ec0 100644 --- a/docs/reference/selectFeatures.html +++ b/docs/reference/selectFeatures.html @@ -78,7 +78,7 @@ celda - 1.11.0 + 1.12.0 diff --git a/docs/reference/semiPheatmap.html b/docs/reference/semiPheatmap.html index 4658259c..9b9e966e 100644 --- a/docs/reference/semiPheatmap.html +++ b/docs/reference/semiPheatmap.html @@ -79,7 +79,7 @@ celda - 1.11.0 + 1.12.0 diff --git a/docs/reference/simulateCells.html b/docs/reference/simulateCells.html index bd6786f9..0428b01b 100644 --- a/docs/reference/simulateCells.html +++ b/docs/reference/simulateCells.html @@ -78,7 +78,7 @@ celda - 1.11.0 + 1.12.0 diff --git a/docs/reference/simulateContamination.html b/docs/reference/simulateContamination.html index b054ec54..fe1f73a0 100644 --- a/docs/reference/simulateContamination.html +++ b/docs/reference/simulateContamination.html @@ -75,7 +75,7 @@ celda - 1.11.0 + 1.12.0 diff --git a/docs/reference/splitModule.html b/docs/reference/splitModule.html index 8ac186e1..38ba4de7 100644 --- a/docs/reference/splitModule.html +++ b/docs/reference/splitModule.html @@ -74,7 +74,7 @@ celda - 1.11.0 + 1.12.0 diff --git a/docs/reference/subsetCeldaList.html b/docs/reference/subsetCeldaList.html index 712dc4a8..7702cc5f 100644 --- a/docs/reference/subsetCeldaList.html +++ b/docs/reference/subsetCeldaList.html @@ -77,7 +77,7 @@ celda - 1.11.0 + 1.12.0 diff --git a/docs/reference/topRank.html b/docs/reference/topRank.html index 77117c04..7fba329c 100644 --- a/docs/reference/topRank.html +++ b/docs/reference/topRank.html @@ -74,7 +74,7 @@ celda - 1.11.0 + 1.12.0 diff --git a/vignettes/articles/celda_pbmc3k.Rmd b/vignettes/articles/celda_pbmc3k.Rmd index 108c3111..baecf4d5 100644 --- a/vignettes/articles/celda_pbmc3k.Rmd +++ b/vignettes/articles/celda_pbmc3k.Rmd @@ -157,7 +157,7 @@ plotGridSearchPerplexity(moduleSplit, altExpName = altExpName, sep = 10) The perplexity alone often does not show a clear elbow or "leveling off". However, the rate of perplexity change (RPC) can be more informative to determine when adding new modules does not add much additional information [Zhao et al., 2015](https://doi.org/10.1186/1471-2105-16-S13-S8){target="_blank"}). An RPC closer to zero indicates that the addition of new modules or cell clusters is not substantially decreasing the perplexity. The RPC of models can be visualized using function `plotRPC`: ```{r module_split_rpc, message = FALSE, warning = FALSE} -plotRPC(moduleSplit, altExpName = altExpName, sep = 10, n = 30) +plotRPC(moduleSplit, altExpName = altExpName) ``` In this case, we will choose an `L` of 80 as the RPC curve tends to level off at this point:

sep

Numeric. Breaks in the x axis of the resulting plot.
n

Integer. Width of the rolling window. Default 10.

alpha

Numeric. Passed to geom_jitter. Opacity of the points. @@ -192,19 +186,19 @@

Arg

Value

-

A ggplot plot object showing perplexity diferences as a function of +

A ggplot plot object showing perplexity differences as a function of clustering parameters.

Examples

data(sceCeldaCGGridSearch)
 sce <- resamplePerplexity(sceCeldaCGGridSearch)
-plotRPC(sce, n = 1)
+plotRPC(sce)
 
data(celdaCGSim, celdaCGGridSearchRes)
 ## Run various combinations of parameters with 'celdaGridSearch'
 celdaCGGridSearchRes <- resamplePerplexity(
   celdaCGSim$counts,
   celdaCGGridSearchRes)
-plotRPC(celdaCGGridSearchRes, n = 1)
+plotRPC(celdaCGGridSearchRes)
diff --git a/docs/reference/recodeClusterZ.html b/docs/reference/recodeClusterZ.html index 71e44b10..b7ea8be3 100644 --- a/docs/reference/recodeClusterZ.html +++ b/docs/reference/recodeClusterZ.html @@ -73,7 +73,7 @@ celda - 1.11.0 + 1.12.0 diff --git a/docs/reference/recursiveSplitCell-1.png b/docs/reference/recursiveSplitCell-1.png index 159edb84..a3dc5dd4 100644 Binary files a/docs/reference/recursiveSplitCell-1.png and b/docs/reference/recursiveSplitCell-1.png differ diff --git a/docs/reference/recursiveSplitCell-2.png b/docs/reference/recursiveSplitCell-2.png index 40e99a58..9608f946 100644 Binary files a/docs/reference/recursiveSplitCell-2.png and b/docs/reference/recursiveSplitCell-2.png differ diff --git a/docs/reference/recursiveSplitCell-3.png b/docs/reference/recursiveSplitCell-3.png index c308bda8..2a1389a1 100644 Binary files a/docs/reference/recursiveSplitCell-3.png and b/docs/reference/recursiveSplitCell-3.png differ diff --git a/docs/reference/recursiveSplitCell-4.png b/docs/reference/recursiveSplitCell-4.png index a51fe126..0650c05c 100644 Binary files a/docs/reference/recursiveSplitCell-4.png and b/docs/reference/recursiveSplitCell-4.png differ diff --git a/docs/reference/recursiveSplitCell.html b/docs/reference/recursiveSplitCell.html index 01460cd1..b567b457 100644 --- a/docs/reference/recursiveSplitCell.html +++ b/docs/reference/recursiveSplitCell.html @@ -81,7 +81,7 @@ celda - 1.11.0 + 1.12.0 @@ -180,9 +180,7 @@

Recursive cell splitting

seed = 12345, perplexity = TRUE, doResampling = FALSE, - doSubsampling = TRUE, numResample = 5, - numSubsample = 5000, logfile = NULL, verbose = TRUE ) @@ -206,9 +204,7 @@

Recursive cell splitting

seed = 12345, perplexity = TRUE, doResampling = FALSE, - doSubsampling = TRUE, numResample = 5, - numSubsample = 5000, logfile = NULL, verbose = TRUE ) @@ -232,9 +228,7 @@

Recursive cell splitting

seed = 12345, perplexity = TRUE, doResampling = FALSE, - doSubsampling = TRUE, numResample = 5, - numSubsample = 5000, logfile = NULL, verbose = TRUE ) @@ -344,23 +338,12 @@

Arg

Boolean. If TRUE, then each cell in the counts matrix will be resampled according to a multinomial distribution to introduce noise before calculating perplexity. Default FALSE.

doSubsampling

Boolean. If TRUE, then a subset of cells from -the original counts matrix will be randomly selected. Default TRUE.
numResample

Integer. The number of times to resample the counts matrix -for evaluating perplexity if doSubsampling is set to TRUE. +for evaluating perplexity if doResampling is set to TRUE. Default 5.

numSubsample

Integer. The number of cells to sample from the -the counts matrix if doSubsampling is set to TRUE. -Default 5000.
logfile

Boolean. If TRUE, then each cell in the counts matrix will be resampled according to a multinomial distribution to introduce noise before calculating perplexity. Default FALSE.

doSubsampling

Boolean. If TRUE, then a subset of cells from -the original counts matrix will be randomly selected. Default TRUE.
numResample

Integer. The number of times to resample the counts matrix -for evaluating perplexity if doSubsampling is set to TRUE. +for evaluating perplexity if doResampling is set to TRUE. Default 5.

numSubsample

Integer. The number of cells to sample from the -the counts matrix if doSubsampling is set to TRUE. -Default 5000.
verbose

Boolean. If TRUE, then each cell in the counts matrix will be resampled according to a multinomial distribution to introduce noise before calculating perplexity. Default FALSE.

doSubsampling

Boolean. If TRUE, then a subset of cells from -the original counts matrix will be randomly selected. Default TRUE.
numResample

Integer. The number of times to resample the counts matrix -for evaluating perplexity if doSubsampling is set to TRUE. +for evaluating perplexity if doResampling is set to TRUE. Default 5.

numSubsample

Integer. The number of cells to sample from the -the counts matrix if doSubsampling is set to TRUE. -Default 5000.
seed