Galfrè Silvia Giulia
| Snapshot Date: 2025-11-18 13:40 -0500 (Tue, 18 Nov 2025) |
| git_url: https://git.bioconductor.org/packages/COTAN |
| git_branch: devel |
| git_last_commit: cf71097 |
| git_last_commit_date: 2025-10-29 11:14:37 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-11-19 10:13 -0500 (Wed, 19 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4827 |
| lconway | macOS 12.7.6 Monterey | x86_64 | R Under development (unstable) (2025-10-21 r88958) -- "Unsuffered Consequences" | 4600 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4564 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 450/2325 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| COTAN 2.11.0 (landing page) Galfrè Silvia Giulia
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
|
To the developers/maintainers of the COTAN package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/COTAN.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: COTAN |
| Version: 2.11.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:COTAN.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings COTAN_2.11.0.tar.gz |
| StartedAt: 2025-11-18 20:17:18 -0500 (Tue, 18 Nov 2025) |
| EndedAt: 2025-11-18 20:39:07 -0500 (Tue, 18 Nov 2025) |
| EllapsedTime: 1308.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: COTAN.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:COTAN.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings COTAN_2.11.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/COTAN.Rcheck’
* using R Under development (unstable) (2025-10-21 r88958)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘COTAN/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘COTAN’ version ‘2.11.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 26 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable. Move as many as possible to Suggests and
use conditionally.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘COTAN’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
UniformClusters 66.103 1.676 67.193
CalculatingCOEX 52.940 0.987 54.213
HandlingClusterizations 41.858 1.055 42.730
HeatmapPlots 31.107 0.830 32.184
ParametersEstimations 21.679 0.645 22.498
COTAN_ObjectCreation 11.494 0.281 11.842
GenesStatistics 10.609 0.384 10.881
Conversions 4.909 0.114 5.044
RawDataCleaning 4.700 0.306 4.818
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘outputTestDatasetCreation.R’
Running ‘spelling.R’
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
COTAN.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL COTAN ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library’ * installing *source* package ‘COTAN’ ... ** this is package ‘COTAN’ version ‘2.11.0’ ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (COTAN)
COTAN.Rcheck/tests/outputTestDatasetCreation.Rout
R Under development (unstable) (2025-10-21 r88958) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
>
> # Creates the files to be reloaded by the tests for comparisons
>
> outputTestDatasetCreation <-
+ function(testsDir = file.path("tests", "testthat")) {
+ utils::data("test.dataset", package = "COTAN")
+ options(parallelly.fork.enable = TRUE)
+ setLoggingLevel(3L)
+
+ obj <- COTAN(raw = test.dataset)
+ obj <- initializeMetaDataset(objCOTAN = obj, GEO = " ",
+ sequencingMethod = "artificial",
+ sampleCondition = "test")
+
+ obj <- proceedToCoex(objCOTAN = obj, cores = 6L, saveObj = FALSE)
+
+ if (FALSE) {
+ saveRDS(obj, file = file.path(testsDir,"test.COTAN.RDS"))
+ }
+
+ cells.names.test <-
+ getCells(objCOTAN = obj)[c(1L:10L, 591L:610L, 991L:1000L)]
+ genes.names.test <-
+ getGenes(objCOTAN = obj)[c(131L:140L, 291L:310L, 591L: 600L)]
+ saveRDS(cells.names.test, file.path(testsDir, "cells.names.test.RDS"))
+ saveRDS(genes.names.test, file.path(testsDir, "genes.names.test.RDS"))
+
+ pcaRaw <- runPCA(x = getRawData(objCOTAN = obj), rank = 10L,
+ BSPARAM = IrlbaParam(), get.rotation = FALSE)[["x"]]
+
+ pca.raw.test <- pcaRaw[genes.names.test, ]
+ saveRDS(pca.raw.test, file.path(testsDir, "pca.raw.test.RDS"))
+
+ dispersion.test <- getDispersion(objCOTAN = obj)[genes.names.test]
+ saveRDS(dispersion.test, file.path(testsDir, "dispersion.test.RDS"))
+
+ raw.norm.test <-
+ getNuNormData(objCOTAN = obj)[genes.names.test, cells.names.test]
+ saveRDS(raw.norm.test, file.path(testsDir, "raw.norm.test.RDS"))
+
+ coex.test <-
+ getGenesCoex(objCOTAN = obj, genes = genes.names.test, zeroDiagonal = FALSE)
+ saveRDS(coex.test, file.path(testsDir, "coex.test.RDS"))
+
+ lambda.test <- getLambda(objCOTAN = obj)[genes.names.test]
+ saveRDS(lambda.test, file.path(testsDir, "lambda.test.RDS"))
+
+ GDI.test <- calculateGDI(objCOTAN = obj)
+ GDI.test <- GDI.test[genes.names.test, ]
+ saveRDS(GDI.test, file.path(testsDir, "GDI.test.RDS"))
+
+ nu.test <- getNu(objCOTAN = obj)[cells.names.test]
+ saveRDS(nu.test, file.path(testsDir, "nu.test.RDS"))
+
+ pvalues.test <- calculatePValue(objCOTAN = obj,
+ geneSubsetCol = genes.names.test,
+ geneSubsetRow = genes.names.test)
+ saveRDS(pvalues.test, file.path(testsDir, "pvalues.test.RDS"))
+
+ groupMarkers <- list(G1 = c("g-000010", "g-000020", "g-000138"),
+ G2 = c("g-000300", "g-000330", "g-000660"),
+ G3 = c("g-000510", "g-000530", "g-000550",
+ "g-000570", "g-000590"))
+
+ gcsData <- genesCoexSpace(objCOTAN = obj,
+ primaryMarkers = unlist(groupMarkers),
+ numGenesPerMarker = 11L)
+
+ genes.coex.space.test <- gcsData[["GCS"]]
+ saveRDS(genes.coex.space.test,
+ file.path(testsDir, "genes.coex.space.test.RDS"))
+
+ genesClustersData <-
+ establishGenesClusters(objCOTAN = obj,
+ groupMarkers = groupMarkers,
+ numGenesPerMarker = 11L,
+ kCuts = 6L, distance = "cosine",
+ hclustMethod = "ward.D2")
+
+ pca.genes.clusters.test <- genesClustersData[["pca_clusters"]]
+ saveRDS(pca.genes.clusters.test,
+ file.path(testsDir, "pca.genes.clusters.test.RDS"))
+
+ # Make it a less strict check as it is only for testing
+ checker <- new("AdvancedGDIUniformityCheck")
+ checker <- shiftCheckerThresholds(checker, 0.1)
+
+ initialResolution <- 1.3
+ splitData <- cellsUniformClustering(objCOTAN = obj,
+ checker = checker,
+ initialResolution = initialResolution,
+ useCoexEigen = TRUE,
+ dataMethod = "LL",
+ numReducedComp = 50L,
+ cores = 6L, optimizeForSpeed = TRUE,
+ deviceStr = "cuda", saveObj = FALSE)
+
+ split.clusters.test <- splitData[["clusters"]]
+ saveRDS(split.clusters.test,
+ file = file.path(testsDir, "split.clusters.test.RDS"))
+
+ test.dataset.clusters1 <- split.clusters.test
+ save(test.dataset.clusters1, compress = TRUE,
+ file = file.path("data", "test.dataset.clusters1.rda"))
+
+ obj <- addClusterization(objCOTAN = obj,
+ clName = "split",
+ clusters = splitData[["clusters"]],
+ coexDF = splitData[["coex"]])
+
+ coex.clusters.test <- splitData[["coex"]][genes.names.test, ]
+ saveRDS(coex.clusters.test, file.path(testsDir, "coex.clusters.test.RDS"))
+
+ pvalDF <- pValueFromDEA(splitData[["coex"]],
+ getNumCells(objCOTAN = obj),
+ adjustmentMethod = "none")
+
+ pvalues.clusters.test <- pvalDF[genes.names.test, ]
+ saveRDS(pvalues.clusters.test,
+ file.path(testsDir, "pvalues.clusters.test.RDS"))
+
+ mergedData <- mergeUniformCellsClusters(objCOTAN = obj,
+ clusters = splitData[["clusters"]],
+ checkers = checker,
+ batchSize = 1L,
+ cores = 6L,
+ distance = "cosine",
+ hclustMethod = "ward.D2",
+ saveObj = FALSE)
+
+ merge.clusters.test <- mergedData[["clusters"]]
+ saveRDS(merge.clusters.test,
+ file = file.path(testsDir, "merge.clusters.test.RDS"))
+
+ test.dataset.clusters2 <- merge.clusters.test
+ save(test.dataset.clusters2, compress = TRUE,
+ file = file.path("data", "test.dataset.clusters2.rda"))
+
+ obj <- addClusterization(objCOTAN = obj,
+ clName = "merge",
+ clusters = mergedData[["clusters"]],
+ coexDF = mergedData[["coex"]])
+ }
>
> proc.time()
user system elapsed
0.258 0.089 0.384
COTAN.Rcheck/tests/spelling.Rout
R Under development (unstable) (2025-10-21 r88958) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> if (requireNamespace("spelling", quietly = TRUE))
+ spelling::spell_check_test(vignettes = TRUE, error = FALSE,
+ skip_on_cran = TRUE)
All Done!
>
> proc.time()
user system elapsed
0.207 0.088 0.328
COTAN.Rcheck/tests/testthat.Rout
R Under development (unstable) (2025-10-21 r88958) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> Sys.setenv(R_TESTS = "")
> library(testthat)
> library(COTAN)
> library(zeallot)
> test_check("COTAN")
Setting new log level to 4
Initializing `COTAN` meta-data
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [10] genes and [20] cells
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 5 iterations
Total calculations elapsed time: 1.83879518508911
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.903596292963576 | max: 4.67949426963453 | % negative: 10
Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 2.62580704689026
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.000830888748168945
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0079200267791748
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.845767021179199
Total calculations elapsed time: 3.4803249835968
Calculate genes' COEX (legacy): DONE
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [10] genes and [20] cells
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 5 genes batches
Parallel dispersion Newton-Raphson: used up to 5 iterations
Parallel dispersion Newton-Raphson: used up to 4 iterations
Parallel dispersion Newton-Raphson: used up to 5 iterations
Parallel dispersion Newton-Raphson: used up to 5 iterations
Parallel dispersion Newton-Raphson: used up to 5 iterations
Total calculations elapsed time: 5.07736110687256
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.903596292963576 | max: 4.67949426963453 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 7 cells batches
Total calculations elapsed time: 0.816920042037964
Estimate `nu`: DONE
`nu` change (abs) | max: 1.75595238095238 | median: 1.07156808035714 | mean: 1.07156808035714
Estimate `dispersion`/`nu`: START
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 5 iterations
Total calculations elapsed time: 1.60614800453186
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 1.03734183779544 | max: 4.61112297272667 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Total calculations elapsed time: 0.854104995727539
Estimate `nu`: DONE
`nu` change (abs) | max: 0.0295487661210321 | median: 0.016072261901129 | mean: 0.016072261901129
`nu` mean: 1.69786080481514
Marginal errors | max: 1.95799528047999 | median 1.32268477389029 | mean: 1.33563364783916
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 5 iterations
Total calculations elapsed time: 1.79769396781921
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.0585450475968788 | max: 3.52739274166646 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Total calculations elapsed time: 0.848936080932617
Estimate `nu`: DONE
`nu` change (abs) | max: 0.417150556912302 | median: 0.240156504520849 | mean: 0.240156504520849
`nu` mean: 0.823005947608547
Marginal errors | max: 0.837672524335755 | median 0.704691669139065 | mean: 0.646575831699997
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 5 iterations
Total calculations elapsed time: 1.6900999546051
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.328845855849147 | max: 4.03031691940854 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Total calculations elapsed time: 0.913403034210205
Estimate `nu`: DONE
`nu` change (abs) | max: 0.164439840041 | median: 0.0957105992188852 | mean: 0.0957105992188852
`nu` mean: 1.06872924082212
Marginal errors | max: 0.260109847946692 | median 0.21392791155499 | mean: 0.197565106613054
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 5 iterations
Total calculations elapsed time: 1.83469200134277
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.229469002841045 | max: 3.87206403670079 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Total calculations elapsed time: 0.900860071182251
Estimate `nu`: DONE
`nu` change (abs) | max: 0.05539667181205 | median: 0.0321044921874999 | mean: 0.0321044921874999
`nu` mean: 0.97670782037545
Marginal errors | max: 0.095347789718808 | median 0.0796003827042702 | mean: 0.0725509735761708
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 5 iterations
Total calculations elapsed time: 1.68722319602966
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.263830434255107 | max: 3.92953043775907 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Total calculations elapsed time: 0.868693113327026
Estimate `nu`: DONE
`nu` change (abs) | max: 0.0196209299693411 | median: 0.0114037947200925 | mean: 0.0114037947200925
`nu` mean: 1.00821713524925
Marginal errors | max: 0.0329495161656741 | median 0.0273479725376307 | mean: 0.0250296751521303
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 5 iterations
Total calculations elapsed time: 1.78986787796021
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.251734659898778 | max: 3.9096133246649 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Total calculations elapsed time: 0.903460025787354
Estimate `nu`: DONE
`nu` change (abs) | max: 0.0069104540740097 | median: 0.0040109538496062 | mean: 0.0040109538496062
`nu` mean: 0.997100499775596
Marginal errors | max: 0.0116950057438405 | median 0.00972280144874116 | mean: 0.00889105008777591
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 5 iterations
Total calculations elapsed time: 1.70872092247009
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.256009779031907 | max: 3.91667271750655 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Total calculations elapsed time: 0.885210990905762
Estimate `nu`: DONE
`nu` change (abs) | max: 0.00251004753849005 | median: 0.00146484374999994 | mean: 0.00146484374999994
`nu` mean: 1.00104520378849
Marginal errors | max: 0.00430755646112857 | median 0.00358203399504298 | mean: 0.00327684342604027
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 5 iterations
Total calculations elapsed time: 1.72405791282654
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.254429717857093 | max: 3.91406908073254 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Total calculations elapsed time: 0.928181886672974
Estimate `nu`: DONE
`nu` change (abs) | max: 0.00104629156456748 | median: 0.000592910406456731 | mean: 0.000592910406456731
`nu` mean: 0.999546618841889
Marginal errors | max: 0.00162038706091039 | median 0.00134441676098973 | mean: 0.00123030512553282
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 5 iterations
Total calculations elapsed time: 1.71165108680725
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.255022049769696 | max: 3.91504587939868 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Total calculations elapsed time: 0.87310004234314
Estimate `nu`: DONE
`nu` change (abs) | max: 0.000418450901304768 | median: 0.000244140625000028 | mean: 0.000244140625000028
`nu` mean: 1.0001743102763
Marginal errors | max: 0.00071569233034019 | median 0.000597297218559056 | mean: 0.000545906995079193
Total calculations elapsed time: 46.9759831428528
Estimate `dispersion`/`nu`: DONE
Estimate `dispersion`/`nu`: START
Initializing `COTAN` meta-data
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [10] genes and [20] cells
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 5 iterations
Total calculations elapsed time: 1.75441408157349
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.903596292963576 | max: 4.67949426963453 | % negative: 10
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not available yet
Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 2.73834204673767
Calculating genes' COEX normalization factor
Fraction of genes' with very low expected contingency tables: 0.181818181818182
Calculate genes' normalization factor elapsed time: 0.00098109245300293
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.00345087051391602
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.967642068862915
Total calculations elapsed time: 3.7104160785675
Calculate genes' COEX (legacy): DONE
Calculate cells' COEX (legacy): START
Retrieving expected cells' contingency table
calculating NN.. done
calculating YN..NY..YY..t().. done
Expected cells' contingency table elapsed time: 2.741947889328
Calculating cells' COEX normalization factor
Fraction of cells' with very low expected contingency tables: 0
Calculate cells' normalization factor elapsed time: 0.000890970230102539
Retrieving observed cells' yes/yes contingency table
calculating YY.. done
Observed cells' contingency table elapsed time: 0.00258016586303711
Estimating cells' COEX
Calculate cells' COEX elapsed time: 0.948843002319336
Total calculations elapsed time: 3.69426202774048
Calculate cells' COEX (legacy): DONE
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Total calculations elapsed time: 0.0135998725891113
Calculate `GDI`: DONE
Total calculations elapsed time: 2.80131196975708
Calculate GDI dataframe: DONE
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Total calculations elapsed time: 0.00366091728210449
Calculate `GDI`: DONE
Total calculations elapsed time: 2.74825406074524
Calculate GDI dataframe: DONE
Included 1 genes with GDI below 1.3
Selected 10 genes using HGDI selector
Running genes' selection: DONE
Running genes' selection: START
Included 1 genes with GDI below 1.3
Selected 10 genes using HGDI selector
Running genes' selection: DONE
Running genes' selection: START
Included 1 genes with GDI below 1.3
Selected 10 genes using HGDI selector
Running genes' selection: DONE
Running genes' selection: START
Selected 5 genes using HGDI selector
Running genes' selection: DONE
Running genes' selection: START
Normalizing layer: counts
Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Finding variable features for layer counts
Calculating gene variances
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Selected 5 genes using HVG_Seurat selector
Running genes' selection: DONE
Running genes' selection: START
Normalizing layer: counts
Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Finding variable features for layer data
Calculating gene means
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating gene variance to mean ratios
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Running genes' selection: START
Given 5 genes as input
Running genes' selection: DONE
Elaborating Reduced dimensionality Data Matrix - START
Running genes' selection: START
Included 1 genes with GDI below 1.3
Selected 10 genes using HGDI selector
Running genes' selection: DONE
Elaborating PCA - START
Elaborating PCA - DONE
Total calculations elapsed time: 1.83373880386353
Elaborating Reduced dimensionality Data Matrix - DONE
Elaborating Reduced dimensionality Data Matrix - START
Running genes' selection: START
Included 1 genes with GDI below 1.3
Selected 10 genes using HGDI selector
Running genes' selection: DONE
Elaborating PCA - START
Elaborating PCA - DONE
Total calculations elapsed time: 1.81582999229431
Elaborating Reduced dimensionality Data Matrix - DONE
Elaborating Reduced dimensionality Data Matrix - START
Running genes' selection: START
Selected 8 genes using HGDI selector
Running genes' selection: DONE
Elaborating PCA - START
Elaborating PCA - DONE
Total calculations elapsed time: 1.76480007171631
Elaborating Reduced dimensionality Data Matrix - DONE
Elaborating Reduced dimensionality Data Matrix - START
Running genes' selection: START
Normalizing layer: counts
Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Finding variable features for layer counts
Calculating gene variances
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Selected 8 genes using HVG_Seurat selector
Running genes' selection: DONE
Elaborating PCA - START
Elaborating PCA - DONE
Total calculations elapsed time: 2.80156183242798
Elaborating Reduced dimensionality Data Matrix - DONE
Elaborating Reduced dimensionality Data Matrix - START
Elaborating COEX Eigen Vectors - START
Elaborating COEX Eigen Vectors - DONE
Total calculations elapsed time: 2.66816401481628
Elaborating Reduced dimensionality Data Matrix - DONE
Elaborating Reduced dimensionality Data Matrix - START
Elaborating COEX Eigen Vectors - START
Elaborating COEX Eigen Vectors - DONE
Total calculations elapsed time: 2.61888694763184
Elaborating Reduced dimensionality Data Matrix - DONE
Initializing `COTAN` meta-data
Initializing `COTAN` meta-data
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [10] genes and [20] cells
Estimate `dispersion`/`nu`: START
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 5 iterations
Total calculations elapsed time: 1.75553297996521
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.903596292963576 | max: 4.67949426963453 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Total calculations elapsed time: 0.887476921081543
Estimate `nu`: DONE
`nu` change (abs) | max: 1.75719246031746 | median: 1.07229953342014 | mean: 1.07229953342014
`nu` mean: 1.68489292689732
Marginal errors | max: 1.735699617106 | median 1.37997441333659 | mean: 1.32181397451301
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 5 iterations
Total calculations elapsed time: 1.80035781860352
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.0655494303592343 | max: 3.54400580804152 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Total calculations elapsed time: 0.927099943161011
Estimate `nu`: DONE
`nu` change (abs) | max: 0.402649984216273 | median: 0.231868788425666 | mean: 0.231868788425666
`nu` mean: 0.829218804209393
Marginal errors | max: 0.803248939260364 | median 0.677504196374571 | mean: 0.619386446933351
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 5 iterations
Total calculations elapsed time: 1.78743410110474
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.326019058449519 | max: 4.02612397202046 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Total calculations elapsed time: 0.874090909957886
Estimate `nu`: DONE
`nu` change (abs) | max: 0.158004893526231 | median: 0.0919692884670312 | mean: 0.0919692884670312
`nu` mean: 1.0660356050592
Marginal errors | max: 0.25067700287536 | median 0.206241644985115 | mean: 0.190402167377958
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 5 iterations
Total calculations elapsed time: 1.72938299179077
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.230397316576369 | max: 3.87365659194104 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Total calculations elapsed time: 0.852938890457153
Estimate `nu`: DONE
`nu` change (abs) | max: 0.0532774732102337 | median: 0.0308837890624999 | mean: 0.0308837890624999
`nu` mean: 0.977606315852266
Marginal errors | max: 0.0916920322976189 | median 0.0765360853958175 | mean: 0.0697673030094085
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 5 iterations
Total calculations elapsed time: 1.6864550113678
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.263457616228195 | max: 3.928924407347 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Total calculations elapsed time: 0.852797985076904
Estimate `nu`: DONE
`nu` change (abs) | max: 0.0187878665732679 | median: 0.0109155550210726 | mean: 0.0109155550210726
`nu` mean: 1.0078723115522
Marginal errors | max: 0.0315207323253404 | median 0.0261635598193228 | mean: 0.0239435763640456
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 5 iterations
Total calculations elapsed time: 1.76259303092957
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.251890641847532 | max: 3.90987172241566 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Total calculations elapsed time: 0.843926191329956
Estimate `nu`: DONE
`nu` change (abs) | max: 0.00649137083358098 | median: 0.00376680890457393 | mean: 0.00376680890457393
`nu` mean: 0.997275438070993
Marginal errors | max: 0.0109748802265024 | median 0.00912386940474885 | mean: 0.00834350038184297
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 5 iterations
Total calculations elapsed time: 1.67954993247986
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.255902752363649 | max: 3.91649655995187 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Total calculations elapsed time: 0.919893026351929
Estimate `nu`: DONE
`nu` change (abs) | max: 0.00230094227000666 | median: 0.00132529141000018 | mean: 0.00132529141000018
`nu` mean: 1.00097565086001
Marginal errors | max: 0.00376864912836616 | median 0.00313421412286186 | mean: 0.00286709489297632
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 5 iterations
Total calculations elapsed time: 1.66575479507446
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.254520292119112 | max: 3.91421850264948 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Total calculations elapsed time: 0.837936878204346
Estimate `nu`: DONE
`nu` change (abs) | max: 0.000837013154366462 | median: 0.000488281250000028 | mean: 0.000488281250000028
`nu` mean: 0.999651268095634
Marginal errors | max: 0.0014405532051498 | median 0.00119489364392944 | mean: 0.0010935543975723
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 5 iterations
Total calculations elapsed time: 1.75020408630371
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.255046800817985 | max: 3.91508667609651 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Total calculations elapsed time: 0.891556024551392
Estimate `nu`: DONE
`nu` change (abs) | max: 0.000418448154490214 | median: 0.000244140624999917 | mean: 0.000244140624999917
`nu` mean: 1.00017430752949
Marginal errors | max: 0.000715683388516908 | median 0.0005972847342397 | mean: 0.00054589991652243
Total calculations elapsed time: 47.3662981987
Estimate `dispersion`/`nu`: DONE
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not available yet
Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 2.61318302154541
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.000486850738525391
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.00122213363647461
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.89045786857605
Total calculations elapsed time: 3.50534987449646
Calculate genes' COEX (legacy): DONE
Calculate cells' COEX (legacy): START
Retrieving expected cells' contingency table
calculating NN.. done
calculating YN..NY..YY..t().. done
Expected cells' contingency table elapsed time: 2.5676531791687
Calculating cells' COEX normalization factor
Calculate cells' normalization factor elapsed time: 0.000775814056396484
Retrieving observed cells' yes/yes contingency table
calculating YY.. done
Observed cells' contingency table elapsed time: 0.00194716453552246
Estimating cells' COEX
Calculate cells' COEX elapsed time: 0.83922290802002
Total calculations elapsed time: 3.40959906578064
Calculate cells' COEX (legacy): DONE
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Total calculations elapsed time: 0.00332903861999512
Calculate `GDI`: DONE
Total calculations elapsed time: 2.52679991722107
Calculate GDI dataframe: DONE
Calculate genes' partial COEX: START
Retrieving expected genes' partial contingency table
calculating partial NN.. done
calculating partial NY..YN..YY.. done
Calculating genes' partial COEX normalization factor
Fraction of genes with very low expected contingency tables: 0.325
Retrieving observed genes' yes/yes partial contingency table
calculating partial YY.. done
Estimating genes' partial COEX
Total calculations elapsed time: 7.02202105522156
Calculate genes' partial COEX: DONE
Calculate cells' partial COEX: START
Retrieving expected cells' partial contingency table
calculating partial NN.. done
calculating partial YN..NY..YY.. done
Calculating cells' partial COEX normalization factor
Fraction of genes with very low expected contingency tables: 0
Retrieving observed cells' yes/yes partial contingency table
calculating partial YY.. done
Estimating cells' partial COEX
Total calculations elapsed time: 7.03970003128052
Calculate cells' partial COEX: DONE
Asked to drop 2 genes and 0 cells
Asked to drop 0 genes and 4 cells
Asked to drop 2 genes and 2 cells
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [10] genes and [20] cells
calculating YY.. done
calculating YY.. done
calculating YN..NY..NN..t().. done
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 3 genes batches
Parallel dispersion Newton-Raphson: used up to 5 iterations
Parallel dispersion Newton-Raphson: used up to 5 iterations
Parallel dispersion Newton-Raphson: used up to 5 iterations
Total calculations elapsed time: 3.56121206283569
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.903596292963576 | max: 4.67949426963453 | % negative: 10
calculating NN.. done
calculating NN.. done
calculating NY..YN..YY..t().. done
Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 2.8737850189209
Calculating genes' COEX normalization factor
Fraction of genes' with very low expected contingency tables: 0.181818181818182
Calculate genes' normalization factor elapsed time: 0.000698089599609375
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.00169992446899414
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.936917066574097
Total calculations elapsed time: 3.8131000995636
Calculate genes' COEX (legacy): DONE
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not available yet
Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 2.76069688796997
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.000787019729614258
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0020749568939209
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.877325057983398
Total calculations elapsed time: 3.6408839225769
Calculate genes' COEX (legacy): DONE
Calculate genes' partial COEX: START
Retrieving expected genes' partial contingency table
calculating partial NN.. done
calculating partial NY..YN..YY.. done
Calculating genes' partial COEX normalization factor
Fraction of genes with very low expected contingency tables: 0.1
Retrieving observed genes' yes/yes partial contingency table
calculating partial YY.. done
Estimating genes' partial COEX
Total calculations elapsed time: 7.25234985351562
Calculate genes' partial COEX: DONE
Calculate genes' partial COEX: START
Retrieving expected genes' partial contingency table
calculating partial NN.. done
calculating partial NY..YN..YY.. done
Calculating genes' partial COEX normalization factor
Fraction of genes with very low expected contingency tables: 0.4
Retrieving observed genes' yes/yes partial contingency table
calculating partial YY.. done
Estimating genes' partial COEX
Total calculations elapsed time: 7.11736106872559
Calculate genes' partial COEX: DONE
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [10] genes and [20] cells
calculating YY.. done
calculating YY.. done
calculating NY..YN..NN..t().. done
Estimate `dispersion`/`nu`: START
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 3 genes batches
Parallel dispersion Newton-Raphson: used up to 5 iterations
Parallel dispersion Newton-Raphson: used up to 5 iterations
Parallel dispersion Newton-Raphson: used up to 5 iterations
Total calculations elapsed time: 3.65635800361633
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.903596292963576 | max: 4.67949426963453 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 5 cells batches
Total calculations elapsed time: 0.956331014633179
Estimate `nu`: DONE
`nu` change (abs) | max: 1.75719246031746 | median: 1.07229953342014 | mean: 1.07229953342014
`nu` mean: 1.68489292689732
Marginal errors | max: 0.255290533439036 | median 0.0807313765005375 | mean: 0.101968565509113
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 3 genes batches
Parallel dispersion Newton-Raphson: used up to 5 iterations
Parallel dispersion Newton-Raphson: used up to 5 iterations
Parallel dispersion Newton-Raphson: used up to 5 iterations
Total calculations elapsed time: 3.76499390602112
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 1.03709166563768 | max: 4.61069655774133 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 5 cells batches
Total calculations elapsed time: 0.879726886749268
Estimate `nu`: DONE
`nu` change (abs) | max: 0.0273438105507502 | median: 0.0148852611818011 | mean: 0.0148852611818011
`nu` mean: 1.69735147626627
Marginal errors | max: 0.00330148418741594 | median 0.00111713187082163 | mean: 0.00132007186542964
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 3 genes batches
Parallel dispersion Newton-Raphson: used up to 5 iterations
Parallel dispersion Newton-Raphson: used up to 5 iterations
Parallel dispersion Newton-Raphson: used up to 5 iterations
Total calculations elapsed time: 3.51761603355408
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 1.03887279473672 | max: 4.60974134092906 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 5 cells batches
Total calculations elapsed time: 0.875622034072876
Estimate `nu`: DONE
`nu` change (abs) | max: 0 | median: 0 | mean: 0
`nu` mean: 1.69735147626627
Marginal errors | max: 5.14174422185931e-05 | median 1.6818224857218e-07 | mean: 5.57649710835051e-06
Total calculations elapsed time: 21.7352440357208
Estimate `dispersion`/`nu`: DONE
calculating NN.. done
calculating NN.. done
calculating YN..NY..YY..t().. done
Calculate cells' COEX (legacy): START
Retrieving expected cells' contingency table
calculating NN.. done
calculating YN..NY..YY..t().. done
Expected cells' contingency table elapsed time: 2.61536979675293
Calculating cells' COEX normalization factor
Fraction of cells' with very low expected contingency tables: 0
Calculate cells' normalization factor elapsed time: 0.0010840892791748
Retrieving observed cells' yes/yes contingency table
calculating YY.. done
Observed cells' contingency table elapsed time: 0.00167989730834961
Estimating cells' COEX
Calculate cells' COEX elapsed time: 0.951942205429077
Total calculations elapsed time: 3.57007598876953
Calculate cells' COEX (legacy): DONE
Calculate cells' partial COEX: START
Retrieving expected cells' partial contingency table
calculating partial NN.. done
calculating partial YN..NY..YY.. done
Calculating cells' partial COEX normalization factor
Fraction of genes with very low expected contingency tables: 0
Retrieving observed cells' yes/yes partial contingency table
calculating partial YY.. done
Estimating cells' partial COEX
Total calculations elapsed time: 7.64944911003113
Calculate cells' partial COEX: DONE
Calculate cells' partial COEX: START
Retrieving expected cells' partial contingency table
calculating partial NN.. done
calculating partial YN..NY..YY.. done
Calculating cells' partial COEX normalization factor
Fraction of genes with very low expected contingency tables: 0
Retrieving observed cells' yes/yes partial contingency table
calculating partial YY.. done
Estimating cells' partial COEX
Total calculations elapsed time: 7.48232007026672
Calculate cells' partial COEX: DONE
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [10] genes and [20] cells
Estimate `dispersion`/`nu`: START
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 3 genes batches
Parallel dispersion Newton-Raphson: used up to 5 iterations
Parallel dispersion Newton-Raphson: used up to 5 iterations
Parallel dispersion Newton-Raphson: used up to 5 iterations
Total calculations elapsed time: 3.64488101005554
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.903596292963576 | max: 4.67949426963453 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 5 cells batches
Total calculations elapsed time: 0.918263912200928
Estimate `nu`: DONE
`nu` change (abs) | max: 1.75719246031746 | median: 1.07229953342014 | mean: 1.07229953342014
`nu` mean: 1.68489292689732
Marginal errors | max: 0.255290533439036 | median 0.0807313765005375 | mean: 0.101968565509113
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 3 genes batches
Parallel dispersion Newton-Raphson: used up to 5 iterations
Parallel dispersion Newton-Raphson: used up to 5 iterations
Parallel dispersion Newton-Raphson: used up to 5 iterations
Total calculations elapsed time: 3.66949200630188
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 1.03709166563768 | max: 4.61069655774133 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 5 cells batches
Total calculations elapsed time: 0.903441190719604
Estimate `nu`: DONE
`nu` change (abs) | max: 0.0273438105507502 | median: 0.0148852611818011 | mean: 0.0148852611818011
`nu` mean: 1.69735147626627
Marginal errors | max: 0.00330148418741594 | median 0.00111713187082163 | mean: 0.00132007186542964
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 3 genes batches
Parallel dispersion Newton-Raphson: used up to 5 iterations
Parallel dispersion Newton-Raphson: used up to 5 iterations
Parallel dispersion Newton-Raphson: used up to 5 iterations
Total calculations elapsed time: 3.60280799865723
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 1.03887279473672 | max: 4.60974134092906 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 5 cells batches
Total calculations elapsed time: 0.880023002624512
Estimate `nu`: DONE
`nu` change (abs) | max: 0 | median: 0 | mean: 0
`nu` mean: 1.69735147626627
Marginal errors | max: 5.14174422185931e-05 | median 1.6818224857218e-07 | mean: 5.57649710835051e-06
Total calculations elapsed time: 21.8726589679718
Estimate `dispersion`/`nu`: DONE
Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 2.8598620891571
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.000674962997436523
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.00199294090270996
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.965320110321045
Total calculations elapsed time: 3.8278501033783
Calculate genes' COEX (legacy): DONE
Calculating S: START
Calculating S: DONE
Calculating G: START
calculating YY.. done
calculating YN..NY..NN..t().. done
calculating NN.. done
calculating NY..YN..YY..t().. done
Estimating G
Total calculations elapsed time: 6.55566906929016
Calculating G: DONE
Using S
Calculating S: START
Calculating S: DONE
calculating PValues: START
Get p-values genome wide on columns and genome wide on rows
Total calculations elapsed time: 0.00206089019775391
calculating PValues: DONE
Using G
Calculating G: START
calculating YY.. done
calculating YN..NY..NN..t().. done
calculating NN.. done
calculating NY..YN..YY..t().. done
Estimating G
Total calculations elapsed time: 6.47623991966248
Calculating G: DONE
calculating PValues: START
Get p-values on a set of genes on columns and on a set of genes on rows
Total calculations elapsed time: 6.47789788246155
calculating PValues: DONE
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Total calculations elapsed time: 0.00278615951538086
Calculate `GDI`: DONE
Total calculations elapsed time: 2.74544405937195
Calculate GDI dataframe: DONE
Calculate GDI dataframe: START
Using G
Calculating G: START
calculating YY.. done
calculating YN..NY..NN..t().. done
calculating NN.. done
calculating NY..YN..YY..t().. done
Estimating G
Total calculations elapsed time: 6.42937898635864
Calculating G: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Total calculations elapsed time: 0.00242018699645996
Calculate `GDI`: DONE
Total calculations elapsed time: 9.12289214134216
Calculate GDI dataframe: DONE
Calculate `GDI`: START
Calculating S: START
Calculating S: DONE
Effective number of cores used: 1
Executing 1 genes batches
Total calculations elapsed time: 0.00548887252807617
Calculate `GDI`: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Total calculations elapsed time: 0.00423598289489746
Calculate `GDI`: DONE
Initializing `COTAN` meta-data
COTAN dataset analysis: START
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [1000] cells
Dataset cleaning elapsed time: 0.906859159469604
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 7 iterations
Total calculations elapsed time: 1.95666694641113
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.0529252975916502 | max: 462.908586418991 | % negative: 17.3333333333333
Model parameter estimation elapsed time: 2.83484292030334
COTAN genes' COEX estimation: START
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not available yet
Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 3.2087938785553
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.0102250576019287
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0582280158996582
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.917555093765259
Total calculations elapsed time: 4.19480204582214
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 5.14026808738708
Dataset analysis elapsed time: 8.88197016716003
COTAN dataset analysis: DONE
Initializing `COTAN` meta-data
Condition test
n cells 1000
COTAN dataset analysis: START
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [1000] cells
Dataset cleaning elapsed time: 0.911631107330322
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 7 iterations
Total calculations elapsed time: 2.08963203430176
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.0529252975916502 | max: 462.908586418991 | % negative: 17.3333333333333
Model parameter estimation elapsed time: 3.06010007858276
COTAN genes' COEX estimation: START
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not available yet
Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 3.30226683616638
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.0101180076599121
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0597701072692871
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.970067977905273
Total calculations elapsed time: 4.34222292900085
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 5.31140184402466
Dataset analysis elapsed time: 9.28313302993774
COTAN dataset analysis: DONE
Using S
Calculating S: START
Calculating S: DONE
calculating PValues: START
Get p-values on a set of genes on columns and on a set of genes on rows
Total calculations elapsed time: 0.0232968330383301
calculating PValues: DONE
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Total calculations elapsed time: 0.0284240245819092
Calculate `GDI`: DONE
Total calculations elapsed time: 2.99790692329407
Calculate GDI dataframe: DONE
Initializing `COTAN` meta-data
Condition test
n cells 1000
COTAN dataset analysis: START
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [1000] cells
Dataset cleaning elapsed time: 0.938555002212524
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 7 iterations
Total calculations elapsed time: 2.1317720413208
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.0529252975916502 | max: 462.908586418991 | % negative: 17.3333333333333
Model parameter estimation elapsed time: 3.09351515769958
COTAN genes' COEX estimation: START
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not available yet
Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 3.20759105682373
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.00747108459472656
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.138156890869141
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.85854697227478
Total calculations elapsed time: 4.21176600456238
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 5.11905884742737
Dataset analysis elapsed time: 9.15112900733948
COTAN dataset analysis: DONE
Using S
Calculating S: START
Calculating S: DONE
calculating PValues: START
Get p-values on a set of genes on columns and genome wide on rows
Total calculations elapsed time: 0.0188009738922119
calculating PValues: DONE
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Total calculations elapsed time: 0.0312099456787109
Calculate `GDI`: DONE
Total calculations elapsed time: 2.61632490158081
Calculate GDI dataframe: DONE
Initializing `COTAN` meta-data
Condition test
n cells 1000
COTAN dataset analysis: START
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [1000] cells
Dataset cleaning elapsed time: 0.939536094665527
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 7 iterations
Total calculations elapsed time: 2.02255988121033
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.0529252975916502 | max: 462.908586418991 | % negative: 17.3333333333333
Model parameter estimation elapsed time: 2.96097683906555
COTAN genes' COEX estimation: START
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not available yet
Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 3.22741103172302
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.00644779205322266
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0595381259918213
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.867380857467651
Total calculations elapsed time: 4.16077780723572
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 5.09058904647827
Dataset analysis elapsed time: 8.99110198020935
COTAN dataset analysis: DONE
Using S
Calculating S: START
Calculating S: DONE
calculating PValues: START
Get p-values on a set of genes on columns and on a set of genes on rows
Total calculations elapsed time: 0.00626707077026367
calculating PValues: DONE
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Total calculations elapsed time: 0.033318042755127
Calculate `GDI`: DONE
Total calculations elapsed time: 2.81754088401794
Calculate GDI dataframe: DONE
Initializing `COTAN` meta-data
Asked to drop 0 genes and 960 cells
COTAN dataset analysis: START
Asked to drop 83 genes and 0 cells
Genes/cells selection done: dropped [83] genes and [0] cells
Working on [517] genes and [40] cells
Dataset cleaning elapsed time: 0.944108963012695
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 7 iterations
Total calculations elapsed time: 1.71848893165588
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.267567793681876 | max: 101.923257389521 | % negative: 52.6112185686654
Model parameter estimation elapsed time: 2.66534304618835
COTAN genes' COEX estimation not requested
Only genes' COEX elapsed time: 0.865641832351685
Dataset analysis elapsed time: 4.47509384155273
COTAN dataset analysis: DONE
Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 2.75018405914307
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.0046241283416748
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0109908580780029
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.882054090499878
Total calculations elapsed time: 3.64785313606262
Calculate genes' COEX (legacy): DONE
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not available yet
Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 2.71561694145203
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.00460100173950195
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.00905609130859375
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.924324035644531
Total calculations elapsed time: 3.65359807014465
Calculate genes' COEX (legacy): DONE
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not available yet
Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 2.63831901550293
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.00567317008972168
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0108959674835205
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.926747798919678
Total calculations elapsed time: 3.58163595199585
Calculate genes' COEX (legacy): DONE
Hangling COTAN object with condition: test
Using S
Calculating S: START
Calculating S: DONE
calculating PValues: START
Get p-values on a set of genes on columns and on a set of genes on rows
Total calculations elapsed time: 0.00569891929626465
calculating PValues: DONE
Handling genes type: G2
Handling genes type: G3
Initializing `COTAN` meta-data
COTAN dataset analysis: START
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [1000] cells
Clean plots: START
PCA: START
PCA: DONE
Hierarchical clustering: START
Hierarchical clustering: DONE
Total calculations elapsed time: 2.05602693557739
Clean plots: DONE
Dataset cleaning elapsed time: 4.4784300327301
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 7 iterations
Total calculations elapsed time: 2.20311188697815
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.0529252975916502 | max: 462.908586418991 | % negative: 17.3333333333333
Model parameter estimation elapsed time: 3.15768098831177
COTAN genes' COEX estimation: START
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not available yet
Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 3.35712313652039
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.00707793235778809
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0591459274291992
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.899178028106689
Total calculations elapsed time: 4.32252502441406
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 5.26883792877197
Dataset analysis elapsed time: 12.9049489498138
COTAN dataset analysis: DONE
Saving elaborated data locally at: /tmp/Rtmp03zTFp/test.cotan.RDS
Creating new clusterization: START
Elaborating Reduced dimensionality Data Matrix - START
Elaborating COEX Eigen Vectors - START
Elaborating COEX Eigen Vectors - DONE
Total calculations elapsed time: 2.85542607307434
Elaborating Reduced dimensionality Data Matrix - DONE
Computing nearest neighbor graph
Computing SNN
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
Number of nodes: 1000
Number of edges: 44886
Running Louvain algorithm with multilevel refinement...
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Maximum modularity in 10 random starts: 0.4008
Number of communities: 4
Elapsed time: 0 seconds
Used resolution for Seurat clusterization is: 1.3
Total calculations elapsed time: 3.88351511955261
Creating new clusterization: DONE
Creating cells' uniform clustering: START
In iteration 1 the number of cells to re-cluster is 1000 cells belonging to 0 clusters
Asked to drop no genes or cells
Creating new clusterization: START
Elaborating Reduced dimensionality Data Matrix - START
Elaborating COEX Eigen Vectors - START
Elaborating COEX Eigen Vectors - DONE
Total calculations elapsed time: 3.13053417205811
Elaborating Reduced dimensionality Data Matrix - DONE
Computing nearest neighbor graph
Computing SNN
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
Number of nodes: 1000
Number of edges: 36652
Running Louvain algorithm with multilevel refinement...
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Maximum modularity in 10 random starts: 0.3743
Number of communities: 4
Elapsed time: 0 seconds
Used resolution for Seurat clusterization is: 1.3
Total calculations elapsed time: 4.05446004867554
Creating new clusterization: DONE
Creating PDF UMAP in file: /tmp/Rtmp03zTFp/test/reclustering/pdf_umap_1.pdf
UMAP plot: START
Calculating UMAP: START
20:33:55 UMAP embedding parameters a = 0.9922 b = 1.112
20:33:55 Read 1000 rows and found 65 numeric columns
20:33:55 Using Annoy for neighbor search, n_neighbors = 30
20:33:55 Building Annoy index with metric = cosine, n_trees = 50
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
20:33:56 Writing NN index file to temp file /tmp/Rtmp03zTFp/file105517dbbc00a
20:33:56 Searching Annoy index using 1 thread, search_k = 3000
20:33:56 Annoy recall = 100%
20:33:57 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30
20:33:59 Initializing from normalized Laplacian + noise (using RSpectra)
20:33:59 Commencing optimization for 500 epochs, with 39044 positive edges
20:33:59 Using rng type: pcg
Using method 'umap'
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
20:34:01 Optimization finished
Calculating UMAP: DONE
Total calculations elapsed time: 5.90073895454407
UMAP plot: DONE
UMAP plot: START
Calculating UMAP: START
20:34:02 UMAP embedding parameters a = 0.9922 b = 1.112
20:34:02 Read 1000 rows and found 65 numeric columns
20:34:02 Using Annoy for neighbor search, n_neighbors = 30
20:34:02 Building Annoy index with metric = cosine, n_trees = 50
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
20:34:02 Writing NN index file to temp file /tmp/Rtmp03zTFp/file105512027f536
20:34:02 Searching Annoy index using 1 thread, search_k = 3000
20:34:02 Annoy recall = 100%
20:34:03 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30
20:34:05 Initializing from normalized Laplacian + noise (using RSpectra)
20:34:05 Commencing optimization for 500 epochs, with 39044 positive edges
20:34:05 Using rng type: pcg
Using method 'umap'
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
20:34:08 Optimization finished
Calculating UMAP: DONE
Total calculations elapsed time: 6.08998107910156
UMAP plot: DONE
* checking uniformity of cluster '0' of 4 clusters
Asked to drop 0 genes and 687 cells
COTAN dataset analysis: START
Asked to drop 43 genes and 0 cells
Genes/cells selection done: dropped [43] genes and [0] cells
Working on [557] genes and [313] cells
Dataset cleaning elapsed time: 0.988077878952026
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 11 iterations
Total calculations elapsed time: 1.97050809860229
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.126565269702225 | max: 788.372048308528 | % negative: 38.5996409335727
Model parameter estimation elapsed time: 2.91754508018494
COTAN genes' COEX estimation: START
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not available yet
Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 3.04190611839294
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.00724983215332031
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0250990390777588
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.986577987670898
Total calculations elapsed time: 4.06083297729492
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 5.04530096054077
Dataset analysis elapsed time: 8.95092391967773
COTAN dataset analysis: DONE
Checking uniformity for the cluster '01_0000' with 313 cells
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Total calculations elapsed time: 0.0303740501403809
Calculate `GDI`: DONE
Total calculations elapsed time: 3.1074378490448
Calculate GDI dataframe: DONE
Clean plots: START
Total calculations elapsed time: 0.0454239845275879
Clean plots: DONE
GDI plot
Removed 0 low GDI genes (such as the fully-expressed) in GDI plot
Cluster 01_0000, with size 313, is uniform
Cluster 01_0000's shift to uniformity: -0.0175178017151378
class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.397, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.0412926391382406, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.37948219828486, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.407, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.0323159784560144, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.43089123341117, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.5, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0.00179533213644524, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.44383613651629, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.5, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 1, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.47612588512221, isUniform = TRUE, clusterSize = 313
cluster 01_0000 is uniform
* checking uniformity of cluster '1' of 4 clusters
Asked to drop 0 genes and 743 cells
COTAN dataset analysis: START
Asked to drop 51 genes and 0 cells
Genes/cells selection done: dropped [51] genes and [0] cells
Working on [549] genes and [257] cells
Dataset cleaning elapsed time: 1.03587198257446
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 10 iterations
Total calculations elapsed time: 2.07753682136536
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.112503099391263 | max: 646.681464270838 | % negative: 40.8014571948998
Model parameter estimation elapsed time: 3.12784910202026
COTAN genes' COEX estimation: START
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not available yet
Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 3.01578593254089
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.00798201560974121
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0248911380767822
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.946197986602783
Total calculations elapsed time: 3.9948570728302
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 4.9840099811554
Dataset analysis elapsed time: 9.14773106575012
COTAN dataset analysis: DONE
Checking uniformity for the cluster '01_0001' with 257 cells
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Total calculations elapsed time: 0.0280270576477051
Calculate `GDI`: DONE
Total calculations elapsed time: 2.95874881744385
Calculate GDI dataframe: DONE
Clean plots: START
Total calculations elapsed time: 0.0446169376373291
Clean plots: DONE
GDI plot
Removed 1 low GDI genes (such as the fully-expressed) in GDI plot
Cluster 01_0001, with size 257, is uniform
Cluster 01_0001's shift to uniformity: -0.0466523594845973
class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.397, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.00910746812386157, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.3503476405154, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.407, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.00728597449908925, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.37278730407692, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.5, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.3866416314687, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.5, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 0, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.45240567481124, isUniform = TRUE, clusterSize = 257
cluster 01_0001 is uniform
* checking uniformity of cluster '2' of 4 clusters
Asked to drop 0 genes and 758 cells
COTAN dataset analysis: START
Asked to drop 77 genes and 0 cells
Genes/cells selection done: dropped [77] genes and [0] cells
Working on [523] genes and [242] cells
Dataset cleaning elapsed time: 0.959603071212769
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 7 iterations
Total calculations elapsed time: 1.90976095199585
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.166254045792573 | max: 224.924342782861 | % negative: 42.6386233269598
Model parameter estimation elapsed time: 2.8580858707428
COTAN genes' COEX estimation: START
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not available yet
Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 3.01816916465759
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.00582098960876465
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0243849754333496
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.959002017974854
Total calculations elapsed time: 4.00737714767456
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 4.92721199989319
Dataset analysis elapsed time: 8.74490094184875
COTAN dataset analysis: DONE
Checking uniformity for the cluster '01_0002' with 242 cells
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Total calculations elapsed time: 0.0231471061706543
Calculate `GDI`: DONE
Total calculations elapsed time: 2.98523616790771
Calculate GDI dataframe: DONE
Clean plots: START
Total calculations elapsed time: 0.0501348972320557
Clean plots: DONE
GDI plot
Removed 2 low GDI genes (such as the fully-expressed) in GDI plot
Cluster 01_0002, with size 242, is uniform
Cluster 01_0002's shift to uniformity: -0.047352793630024
class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.397, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.00764818355640535, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.34964720636998, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.407, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.00764818355640535, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.37472946305404, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.5, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.38771313919655, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.5, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 0, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.43097703442028, isUniform = TRUE, clusterSize = 242
cluster 01_0002 is uniform
* checking uniformity of cluster '3' of 4 clusters
Asked to drop 0 genes and 812 cells
COTAN dataset analysis: START
Asked to drop 79 genes and 0 cells
Genes/cells selection done: dropped [79] genes and [0] cells
Working on [521] genes and [188] cells
Dataset cleaning elapsed time: 1.03596591949463
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 6 iterations
Total calculations elapsed time: 2.14174699783325
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.210007411487223 | max: 67.8701314818729 | % negative: 45.6813819577735
Model parameter estimation elapsed time: 3.15695905685425
COTAN genes' COEX estimation: START
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not available yet
Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 3.18312692642212
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.00585103034973145
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0207231044769287
Estimating genes' COEX
Calculate genes' COEX elapsed time: 1.02293992042542
Total calculations elapsed time: 4.23264098167419
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 5.25021195411682
Dataset analysis elapsed time: 9.4431369304657
COTAN dataset analysis: DONE
Checking uniformity for the cluster '01_0003' with 188 cells
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Total calculations elapsed time: 0.0252161026000977
Calculate `GDI`: DONE
Total calculations elapsed time: 3.05275082588196
Calculate GDI dataframe: DONE
Clean plots: START
Total calculations elapsed time: 0.0492980480194092
Clean plots: DONE
GDI plot
Removed 4 low GDI genes (such as the fully-expressed) in GDI plot
Cluster 01_0003, with size 188, is uniform
Cluster 01_0003's shift to uniformity: -0.0672912272436446
class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.397, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.00383877159309021, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.32970877275636, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.407, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.00191938579654511, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.35752445041519, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.5, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.37495297633951, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.5, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 0, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.40148843025229, isUniform = TRUE, clusterSize = 188
cluster 01_0003 is uniform
Found 4 uniform and 0 non-uniform clusters
Stopping: too few cells left to cluster
Unclustered cell left: 0
The final raw clusterization contains [ 4 ] different clusters: 01_0000, 01_0001, 01_0002, 01_0003
Differential Expression Analysis - START
* DEA on cluster '1' with 313 cells
* DEA on cluster '2' with 257 cells
* DEA on cluster '3' with 242 cells
* DEA on cluster '4' with 188 cells
Total calculations elapsed time: 0.0342288017272949
Differential Expression Analysis - DONE
Applied reordering to clusterization is:
1 -> 3, 2 -> 1, 3 -> 2, 4 -> 4
Total calculations elapsed time: 82.4198749065399
Creating cells' uniform clustering: DONE
Applied reordering to clusterization is:
1 -> 1, 2 -> 2, 3 -> 3, 4 -> 4
Asked to drop 0 genes and 812 cells
COTAN dataset analysis: START
Asked to drop 79 genes and 0 cells
Genes/cells selection done: dropped [79] genes and [0] cells
Working on [521] genes and [188] cells
Dataset cleaning elapsed time: 0.95151686668396
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 6 iterations
Total calculations elapsed time: 2.00032091140747
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.210007411487223 | max: 67.8701314818729 | % negative: 45.6813819577735
Model parameter estimation elapsed time: 2.96674704551697
COTAN genes' COEX estimation: START
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not available yet
Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 3.2112181186676
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.0061800479888916
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0239138603210449
Estimating genes' COEX
Calculate genes' COEX elapsed time: 1.01876497268677
Total calculations elapsed time: 4.26007699966431
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 5.18494296073914
Dataset analysis elapsed time: 9.10320687294006
COTAN dataset analysis: DONE
Checking uniformity for the cluster 'Cluster_4' with 188 cells
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Total calculations elapsed time: 0.0211219787597656
Calculate `GDI`: DONE
Total calculations elapsed time: 3.01753306388855
Calculate GDI dataframe: DONE
Clean plots: START
Total calculations elapsed time: 0.0347261428833008
Clean plots: DONE
GDI plot
Removed 4 low GDI genes (such as the fully-expressed) in GDI plot
Cluster Cluster_4, with size 188, is uniform
Cluster Cluster_4's shift to uniformity: -0.0672912272436446
class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.397, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.00383877159309021, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.32970877275636, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.407, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.00191938579654511, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.35752445041519, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.5, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.37495297633951, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.5, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 0, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.40148843025229, isUniform = TRUE, clusterSize = 188
Differential Expression Analysis - START
* DEA on cluster '-1' with 50 cells
* DEA on cluster '1' with 257 cells
* DEA on cluster '2' with 242 cells
* DEA on cluster '3' with 280 cells
* DEA on cluster '4' with 171 cells
Total calculations elapsed time: 0.0356571674346924
Differential Expression Analysis - DONE
Applied reordering to clusterization is:
1 -> 4, 2 -> 3, 3 -> 2, 4 -> 1, -1 -> -1
Applied reordering to clusterization is:
1 -> 1, 2 -> 2, 3 -> 3, 4 -> 4, -1 -> -1
Creating cells' uniform clustering: START
In iteration 1 the number of cells to re-cluster is 1000 cells belonging to 0 clusters
Asked to drop no genes or cells
Creating new clusterization: START
Elaborating Reduced dimensionality Data Matrix - START
Running genes' selection: START
Normalizing layer: counts
Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Finding variable features for layer counts
Calculating gene variances
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Selected 600 genes using HVG_Seurat selector
Running genes' selection: DONE
Elaborating PCA - START
Elaborating PCA - DONE
Total calculations elapsed time: 3.66052317619324
Elaborating Reduced dimensionality Data Matrix - DONE
Computing nearest neighbor graph
Computing SNN
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
Number of nodes: 1000
Number of edges: 67288
Running Louvain algorithm with multilevel refinement...
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Maximum modularity in 10 random starts: 0.3650
Number of communities: 5
Elapsed time: 0 seconds
Used resolution for Seurat clusterization is: 1.3
Total calculations elapsed time: 4.65482997894287
Creating new clusterization: DONE
Using passed in clusterization
Creating PDF UMAP in file: /tmp/Rtmp03zTFp/test/reclustering/pdf_umap_1.pdf
UMAP plot: START
Calculating UMAP: START
20:35:34 UMAP embedding parameters a = 0.9922 b = 1.112
20:35:34 Read 1000 rows and found 40 numeric columns
20:35:34 Using Annoy for neighbor search, n_neighbors = 30
20:35:34 Building Annoy index with metric = cosine, n_trees = 50
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
20:35:35 Writing NN index file to temp file /tmp/Rtmp03zTFp/file105513ea09332
20:35:35 Searching Annoy index using 1 thread, search_k = 3000
20:35:35 Annoy recall = 100%
20:35:36 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30
20:35:38 Found 2 connected components, falling back to 'spca' initialization with init_sdev = 1
20:35:38 Using 'irlba' for PCA
20:35:38 PCA: 2 components explained 36.15% variance
20:35:38 Scaling init to sdev = 1
20:35:38 Commencing optimization for 500 epochs, with 41630 positive edges
20:35:38 Using rng type: pcg
Using method 'umap'
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
20:35:40 Optimization finished
Calculating UMAP: DONE
Total calculations elapsed time: 5.76962208747864
UMAP plot: DONE
UMAP plot: START
Calculating UMAP: START
20:35:40 UMAP embedding parameters a = 0.9922 b = 1.112
20:35:40 Read 1000 rows and found 40 numeric columns
20:35:40 Using Annoy for neighbor search, n_neighbors = 30
20:35:40 Building Annoy index with metric = cosine, n_trees = 50
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
20:35:41 Writing NN index file to temp file /tmp/Rtmp03zTFp/file10551a8cc9c5
20:35:41 Searching Annoy index using 1 thread, search_k = 3000
20:35:41 Annoy recall = 100%
20:35:42 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30
20:35:44 Found 2 connected components, falling back to 'spca' initialization with init_sdev = 1
20:35:44 Using 'irlba' for PCA
20:35:44 PCA: 2 components explained 36.15% variance
20:35:44 Scaling init to sdev = 1
20:35:44 Commencing optimization for 500 epochs, with 41630 positive edges
20:35:44 Using rng type: pcg
Using method 'umap'
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
20:35:46 Optimization finished
Calculating UMAP: DONE
Total calculations elapsed time: 5.7292001247406
UMAP plot: DONE
* checking uniformity of cluster '1' of 2 clusters
Asked to drop 0 genes and 500 cells
COTAN dataset analysis: START
Asked to drop 38 genes and 0 cells
Genes/cells selection done: dropped [38] genes and [0] cells
Working on [562] genes and [500] cells
Dataset cleaning elapsed time: 1.01418495178223
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 7 iterations
Total calculations elapsed time: 1.89496397972107
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.108871643378045 | max: 295.971778839086 | % negative: 35.0533807829181
Model parameter estimation elapsed time: 2.90623497962952
COTAN genes' COEX estimation: START
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not available yet
Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 3.13825511932373
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.00710582733154297
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0307910442352295
Estimating genes' COEX
Calculate genes' COEX elapsed time: 1.02348613739014
Total calculations elapsed time: 4.19963812828064
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 5.09066200256348
Dataset analysis elapsed time: 9.01108193397522
COTAN dataset analysis: DONE
Checking uniformity for the cluster '01_0001' with 500 cells
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Total calculations elapsed time: 0.0247981548309326
Calculate `GDI`: DONE
Total calculations elapsed time: 2.79518699645996
Calculate GDI dataframe: DONE
Clean plots: START
Total calculations elapsed time: 0.0355031490325928
Clean plots: DONE
GDI plot
Removed 2 low GDI genes (such as the fully-expressed) in GDI plot
Cluster 01_0001, with size 500, is uniform
Cluster 01_0001's shift to uniformity: -0.0417301990665568
class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.397, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.0124555160142349, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.35526980093344, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.407, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.00889679715302491, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.38536328181506, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.5, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.40346106115488, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.5, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 0, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.42565794715045, isUniform = TRUE, clusterSize = 500
cluster 01_0001 is uniform
* checking uniformity of cluster '2' of 2 clusters
Asked to drop 0 genes and 500 cells
COTAN dataset analysis: START
Asked to drop 44 genes and 0 cells
Genes/cells selection done: dropped [44] genes and [0] cells
Working on [556] genes and [500] cells
Dataset cleaning elapsed time: 1.07146787643433
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 7 iterations
Total calculations elapsed time: 2.20051598548889
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.0636486786621688 | max: 141.389145035675 | % negative: 36.1510791366906
Model parameter estimation elapsed time: 3.28288888931274
COTAN genes' COEX estimation: START
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not available yet
Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 3.40509986877441
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.00765013694763184
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0340368747711182
Estimating genes' COEX
Calculate genes' COEX elapsed time: 1.07174706459045
Total calculations elapsed time: 4.51853394508362
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 5.51817512512207
Dataset analysis elapsed time: 9.87253189086914
COTAN dataset analysis: DONE
Checking uniformity for the cluster '01_0002' with 500 cells
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Total calculations elapsed time: 0.0291211605072021
Calculate `GDI`: DONE
Total calculations elapsed time: 3.06947588920593
Calculate GDI dataframe: DONE
Clean plots: START
Total calculations elapsed time: 0.0474340915679932
Clean plots: DONE
GDI plot
Removed 2 low GDI genes (such as the fully-expressed) in GDI plot
Cluster 01_0002, with size 500, is uniform
Cluster 01_0002's shift to uniformity: -0.0413872276843441
class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.397, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.00719424460431655, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.35561277231566, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.407, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.00359712230215827, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.37204026755188, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.5, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.38757136821583, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.5, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 0, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.40876953414106, isUniform = TRUE, clusterSize = 500
cluster 01_0002 is uniform
Found 2 uniform and 0 non-uniform clusters
Stopping: too few cells left to cluster
Unclustered cell left: 0
The final raw clusterization contains [ 2 ] different clusters: 01_0001, 01_0002
Differential Expression Analysis - START
* DEA on cluster '1' with 500 cells
* DEA on cluster '2' with 500 cells
Total calculations elapsed time: 0.0308170318603516
Differential Expression Analysis - DONE
Applied reordering to clusterization is:
1 -> 1, 2 -> 2
Total calculations elapsed time: 50.1123869419098
Creating cells' uniform clustering: DONE
findClustersMarkers - START
Log Fold Change Analysis - START
* Analysis of cluster: '1'
* Analysis of cluster: '2'
* Analysis of cluster: '3'
* Analysis of cluster: '4'
Total calculations elapsed time: 3.97021198272705
Log Fold Change Analysis - DONE
Total calculations elapsed time: 3.98422884941101
findClustersMarkers - DONE
findClustersMarkers - START
Log Fold Change Analysis - START
* Analysis of cluster: '1'
* Analysis of cluster: '2'
* Analysis of cluster: '3'
* Analysis of cluster: '4'
Total calculations elapsed time: 3.88572406768799
Log Fold Change Analysis - DONE
Total calculations elapsed time: 3.89883780479431
findClustersMarkers - DONE
findClustersMarkers - START
Differential Expression Analysis - START
* DEA on cluster '1' with 257 cells
* DEA on cluster '2' with 242 cells
* DEA on cluster '3' with 313 cells
* DEA on cluster '4' with 188 cells
Total calculations elapsed time: 0.0391809940338135
Differential Expression Analysis - DONE
Log Fold Change Analysis - START
* Analysis of cluster: '1'
* Analysis of cluster: '2'
* Analysis of cluster: '3'
* Analysis of cluster: '4'
Total calculations elapsed time: 3.93662190437317
Log Fold Change Analysis - DONE
Total calculations elapsed time: 3.987380027771
findClustersMarkers - DONE
[1] "Tested cluster: 1"
Asked to drop 0 genes and 743 cells
COTAN dataset analysis: START
Asked to drop 51 genes and 0 cells
Genes/cells selection done: dropped [51] genes and [0] cells
Working on [549] genes and [257] cells
Dataset cleaning elapsed time: 1.00983691215515
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 10 iterations
Total calculations elapsed time: 1.96781396865845
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.112503099391263 | max: 646.681464270838 | % negative: 40.8014571948998
Model parameter estimation elapsed time: 2.95859122276306
COTAN genes' COEX estimation: START
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not available yet
Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 3.06187701225281
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.00531411170959473
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0223219394683838
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.983577013015747
Total calculations elapsed time: 4.07309007644653
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 5.06804299354553
Dataset analysis elapsed time: 9.03647112846375
COTAN dataset analysis: DONE
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Total calculations elapsed time: 0.0239059925079346
Calculate `GDI`: DONE
Total calculations elapsed time: 2.83259105682373
Calculate GDI dataframe: DONE
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [10] genes and [20] cells
Initializing `COTAN` meta-data
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [1000] cells
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 7 iterations
Total calculations elapsed time: 2.29491496086121
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.0529252975916502 | max: 462.908586418991 | % negative: 17.3333333333333
Initializing `COTAN` meta-data
COTAN dataset analysis: START
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [1000] cells
Dataset cleaning elapsed time: 1.02455902099609
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 7 iterations
Total calculations elapsed time: 2.05362415313721
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.0529252975916502 | max: 462.908586418991 | % negative: 17.3333333333333
Model parameter estimation elapsed time: 3.03571319580078
COTAN genes' COEX estimation not requested
Only genes' COEX elapsed time: 0.963830947875977
Dataset analysis elapsed time: 5.02410316467285
COTAN dataset analysis: DONE
Normalizing layer: counts
Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Finding variable features for layer counts
Calculating gene variances
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Centering and scaling data matrix
|
| | 0%
|
|======================================================================| 100%
PC_ 1
Positive: g-000397, g-000525, g-000460, g-000458, g-000535, g-000217, g-000194, g-000497, g-000432, g-000383
g-000318, g-000486, g-000464, g-000588, g-000549, g-000368, g-000252, g-000151, g-000209, g-000538
g-000325, g-000514, g-000524, g-000244, g-000320, g-000201, g-000499, g-000309, g-000290, g-000483
Negative: g-000415, g-000506, g-000496, g-000579, g-000572, g-000421, g-000455, g-000328, g-000178, g-000567
g-000405, g-000296, g-000387, g-000501, g-000493, g-000481, g-000343, g-000528, g-000551, g-000414
g-000367, g-000594, g-000159, g-000517, g-000574, g-000229, g-000222, g-000533, g-000243, g-000306
PC_ 2
Positive: g-000141, g-000093, g-000089, g-000033, g-000123, g-000557, g-000330, g-000156, g-000142, g-000095
g-000061, g-000235, g-000032, g-000186, g-000056, g-000259, g-000027, g-000041, g-000333, g-000386
g-000009, g-000395, g-000048, g-000116, g-000340, g-000418, g-000035, g-000332, g-000086, g-000040
Negative: g-000088, g-000158, g-000255, g-000115, g-000054, g-000472, g-000554, g-000391, g-000253, g-000226
g-000051, g-000147, g-000541, g-000077, g-000224, g-000194, g-000290, g-000293, g-000313, g-000118
g-000121, g-000220, g-000467, g-000500, g-000341, g-000039, g-000091, g-000249, g-000426, g-000288
PC_ 3
Positive: g-000126, g-000083, g-000086, g-000117, g-000130, g-000010, g-000498, g-000333, g-000047, g-000179
g-000340, g-000035, g-000531, g-000140, g-000527, g-000049, g-000316, g-000031, g-000014, g-000073
g-000218, g-000445, g-000129, g-000175, g-000105, g-000581, g-000404, g-000025, g-000266, g-000354
Negative: g-000096, g-000575, g-000370, g-000337, g-000319, g-000364, g-000308, g-000293, g-000147, g-000307
g-000038, g-000492, g-000541, g-000185, g-000008, g-000482, g-000562, g-000097, g-000222, g-000084
g-000141, g-000377, g-000224, g-000223, g-000136, g-000434, g-000277, g-000426, g-000139, g-000093
PC_ 4
Positive: g-000006, g-000043, g-000462, g-000279, g-000180, g-000576, g-000087, g-000584, g-000498, g-000333
g-000189, g-000088, g-000451, g-000059, g-000135, g-000281, g-000106, g-000429, g-000316, g-000578
g-000303, g-000031, g-000581, g-000026, g-000122, g-000561, g-000546, g-000164, g-000353, g-000300
Negative: g-000072, g-000012, g-000129, g-000052, g-000097, g-000262, g-000080, g-000056, g-000025, g-000092
g-000354, g-000334, g-000423, g-000228, g-000002, g-000010, g-000086, g-000147, g-000185, g-000172
g-000124, g-000009, g-000077, g-000476, g-000126, g-000145, g-000065, g-000268, g-000152, g-000348
PC_ 5
Positive: g-000051, g-000150, g-000088, g-000476, g-000344, g-000116, g-000428, g-000012, g-000523, g-000394
g-000101, g-000127, g-000069, g-000214, g-000049, g-000357, g-000075, g-000081, g-000576, g-000342
g-000439, g-000018, g-000070, g-000079, g-000015, g-000550, g-000600, g-000247, g-000218, g-000331
Negative: g-000105, g-000037, g-000110, g-000054, g-000090, g-000389, g-000022, g-000578, g-000289, g-000147
g-000547, g-000011, g-000477, g-000433, g-000200, g-000348, g-000404, g-000003, g-000250, g-000109
g-000402, g-000241, g-000595, g-000341, g-000560, g-000385, g-000413, g-000352, g-000573, g-000265
Computing nearest neighbor graph
Computing SNN
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
Number of nodes: 1000
Number of edges: 68112
Running Louvain algorithm with multilevel refinement...
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Maximum modularity in 10 random starts: 0.5999
Number of communities: 3
Elapsed time: 0 seconds
Clusterizations found: RNA_snn_res.0.8, seurat_clusters
Conditions found: orig.ident
COTAN dataset analysis: START
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [1000] cells
Dataset cleaning elapsed time: 0.987260103225708
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 7 iterations
Total calculations elapsed time: 2.14675688743591
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.0529252975916502 | max: 462.908586418991 | % negative: 17.3333333333333
Model parameter estimation elapsed time: 3.05290079116821
COTAN genes' COEX estimation not requested
Only genes' COEX elapsed time: 0.880731105804443
Dataset analysis elapsed time: 4.92089200019836
COTAN dataset analysis: DONE
COTAN dataset analysis: START
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [1000] cells
Dataset cleaning elapsed time: 0.996923923492432
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 7 iterations
Total calculations elapsed time: 2.16913199424744
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.0529252975916502 | max: 462.908586418991 | % negative: 17.3333333333333
Model parameter estimation elapsed time: 3.11791706085205
COTAN genes' COEX estimation: START
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not available yet
Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 3.54795384407043
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.00627517700195312
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0579497814178467
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.999967098236084
Total calculations elapsed time: 4.61214590072632
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 5.65310502052307
Dataset analysis elapsed time: 9.76794600486755
COTAN dataset analysis: DONE
Calculating gene co-expression space - START
Using S
Calculating S: START
Calculating S: DONE
calculating PValues: START
Get p-values on a set of genes on columns and genome wide on rows
Total calculations elapsed time: 0.00463414192199707
calculating PValues: DONE
Number of selected secondary markers: 6
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Total calculations elapsed time: 0.00813698768615723
Calculate `GDI`: DONE
Number of columns (V set - secondary markers): 6
Number of rows (U set): 60
Total calculations elapsed time: 0.990457057952881
Calculating gene co-expression space - DONE
Calculating gene co-expression space - START
Using S
Calculating S: START
Calculating S: DONE
calculating PValues: START
Get p-values on a set of genes on columns and genome wide on rows
Total calculations elapsed time: 0.00687289237976074
calculating PValues: DONE
Number of selected secondary markers: 98
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Total calculations elapsed time: 0.00800800323486328
Calculate `GDI`: DONE
Number of columns (V set - secondary markers): 98
Number of rows (U set): 60
Total calculations elapsed time: 1.02413892745972
Calculating gene co-expression space - DONE
Establishing gene clusters - START
Calculating gene co-expression space - START
Using S
Calculating S: START
Calculating S: DONE
calculating PValues: START
Get p-values on a set of genes on columns and genome wide on rows
Total calculations elapsed time: 0.00698685646057129
calculating PValues: DONE
Number of selected secondary markers: 98
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Total calculations elapsed time: 0.00845789909362793
Calculate `GDI`: DONE
Number of columns (V set - secondary markers): 98
Number of rows (U set): 60
Total calculations elapsed time: 1.04953098297119
Calculating gene co-expression space - DONE
Total calculations elapsed time: 1.13407897949219
Establishing gene clusters - DONE
Initializing `COTAN` meta-data
COTAN dataset analysis: START
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [1000] cells
Dataset cleaning elapsed time: 1.00464010238647
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 7 iterations
Total calculations elapsed time: 2.19677209854126
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.0529252975916502 | max: 462.908586418991 | % negative: 17.3333333333333
Model parameter estimation elapsed time: 3.20658588409424
COTAN genes' COEX estimation not requested
Only genes' COEX elapsed time: 0.96246600151062
Dataset analysis elapsed time: 5.17369198799133
COTAN dataset analysis: DONE
Differential Expression Analysis - START
* DEA on cluster '1' with 257 cells
* DEA on cluster '2' with 242 cells
* DEA on cluster '3' with 313 cells
* DEA on cluster '4' with 188 cells
Total calculations elapsed time: 0.0389490127563477
Differential Expression Analysis - DONE
Log Fold Change Analysis - START
* Analysis of cluster: '1'
* Analysis of cluster: '2'
* Analysis of cluster: '3'
* Analysis of cluster: '4'
Total calculations elapsed time: 3.88307213783264
Log Fold Change Analysis - DONE
clustersDeltaExpression - START
Handling cluster '1' with mean UDE 1.10997640736885
Handling cluster '2' with mean UDE 1.00770245700749
Handling cluster '3' with mean UDE 0.95940682189354
Handling cluster '4' with mean UDE 0.907328369455933
clustersDeltaExpression - DONE
In group G1 there are 3 detected over 3 genes
In group G2 there are 2 detected over 3 genes
In group G3 there are 5 detected over 5 genes
Merging cells' uniform clustering: START
The merge algorithm will use 2 passes
Start merging nearest clusters - the main threshold is: 1.297
Start merging nearest clusters: iteration 1
Differential Expression Analysis - START
* DEA on cluster '1' with 257 cells
* DEA on cluster '2' with 242 cells
* DEA on cluster '3' with 313 cells
* DEA on cluster '4' with 188 cells
Total calculations elapsed time: 0.0380129814147949
Differential Expression Analysis - DONE
Updating check results for the 0 already tested pairs to align to new checker
1 new clusters pairs to be tested for merging:
c("1", "2")
*1_2-merge
Asked to drop 0 genes and 501 cells
COTAN dataset analysis: START
Asked to drop 16 genes and 0 cells
Genes/cells selection done: dropped [16] genes and [0] cells
Working on [584] genes and [499] cells
Dataset cleaning elapsed time: 0.973134994506836
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 10 iterations
Total calculations elapsed time: 2.00714206695557
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.0608154544840047 | max: 1260.06995351592 | % negative: 35.6164383561644
Model parameter estimation elapsed time: 2.93577098846436
COTAN genes' COEX estimation: START
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not available yet
Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 3.07105398178101
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.00615596771240234
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0352330207824707
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.898026943206787
Total calculations elapsed time: 4.01046991348267
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 4.90935492515564
Dataset analysis elapsed time: 8.81826090812683
COTAN dataset analysis: DONE
Checking uniformity for the cluster '1_2-merge' with 499 cells
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Total calculations elapsed time: 0.0308680534362793
Calculate `GDI`: DONE
Total calculations elapsed time: 2.78858399391174
Calculate GDI dataframe: DONE
Clean plots: START
Total calculations elapsed time: 0.0454549789428711
Clean plots: DONE
GDI plot
Removed 1 low GDI genes (such as the fully-expressed) in GDI plot
Cluster 1_2-merge, with size 499, is not uniform
Cluster 1_2-merge's shift to uniformity: 0.0566581136434088
class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.297, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.178082191780822, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.35365811364341, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.307, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.148972602739726, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.37149326865972, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.4, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0.00513698630136986, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.38256306292788, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.4, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 3, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.42111642638126, isUniform = FALSE, clusterSize = 499
Clusters 1 and 2 cannot be merged
Finished the first batch - no merges were executed
Loop calculations elapsed time: 16.3065328598022
Start merging nearest clusters: iteration 2
Differential Expression Analysis - START
* DEA on cluster '1' with 257 cells
* DEA on cluster '2' with 242 cells
* DEA on cluster '3' with 313 cells
* DEA on cluster '4' with 188 cells
Total calculations elapsed time: 0.0336618423461914
Differential Expression Analysis - DONE
Updating check results for the 1 already tested pairs to align to new checker
1 new clusters pairs to be tested for merging:
c("3", "4")
*3_4-merge
Asked to drop 0 genes and 499 cells
COTAN dataset analysis: START
Asked to drop 37 genes and 0 cells
Genes/cells selection done: dropped [37] genes and [0] cells
Working on [563] genes and [501] cells
Dataset cleaning elapsed time: 0.954071044921875
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 11 iterations
Total calculations elapsed time: 1.88558506965637
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.107568326617881 | max: 698.639334552754 | % negative: 32.1492007104796
Model parameter estimation elapsed time: 2.85657691955566
COTAN genes' COEX estimation: START
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not available yet
Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 3.09819293022156
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.00557208061218262
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0398259162902832
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.928784132003784
Total calculations elapsed time: 4.07237505912781
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 4.97190713882446
Dataset analysis elapsed time: 8.782555103302
COTAN dataset analysis: DONE
Checking uniformity for the cluster '3_4-merge' with 501 cells
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Total calculations elapsed time: 0.028576135635376
Calculate `GDI`: DONE
Total calculations elapsed time: 2.92315697669983
Calculate GDI dataframe: DONE
Clean plots: START
Total calculations elapsed time: 0.0422680377960205
Clean plots: DONE
GDI plot
Removed 0 low GDI genes (such as the fully-expressed) in GDI plot
Cluster 3_4-merge, with size 501, is not uniform
Cluster 3_4-merge's shift to uniformity: 0.0813107504723087
class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.297, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.259325044404973, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.37831075047231, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.307, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.216696269982238, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.41473792188165, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.4, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0.0301953818827709, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.43341610223239, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.4, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 17, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.46173948790286, isUniform = FALSE, clusterSize = 501
Clusters 3 and 4 cannot be merged
No clusters will be merged
None of the remaining tested cluster pairs could be merged
Executed all merges for threshold 1.297 out of 2 checks
Start merging nearest clusters - the main threshold is: 1.397
Start merging nearest clusters: iteration 3
Differential Expression Analysis - START
* DEA on cluster '1' with 257 cells
* DEA on cluster '2' with 242 cells
* DEA on cluster '3' with 313 cells
* DEA on cluster '4' with 188 cells
Total calculations elapsed time: 0.0339682102203369
Differential Expression Analysis - DONE
Updating check results for the 2 already tested pairs to align to new checker
1 new clusters pairs to be tested for merging:
c("2", "4")
*2_4-merge
Asked to drop 0 genes and 570 cells
COTAN dataset analysis: START
Asked to drop 9 genes and 0 cells
Genes/cells selection done: dropped [9] genes and [0] cells
Working on [591] genes and [430] cells
Dataset cleaning elapsed time: 0.960336923599243
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 7 iterations
Total calculations elapsed time: 1.98645997047424
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.0739592351622374 | max: 400.051960722886 | % negative: 25.7191201353638
Model parameter estimation elapsed time: 2.96933603286743
COTAN genes' COEX estimation: START
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not available yet
Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 3.10054087638855
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.00675010681152344
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0393249988555908
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.954246997833252
Total calculations elapsed time: 4.10086297988892
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 5.08424711227417
Dataset analysis elapsed time: 9.01392006874084
COTAN dataset analysis: DONE
Checking uniformity for the cluster '2_4-merge' with 430 cells
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Total calculations elapsed time: 0.0303430557250977
Calculate `GDI`: DONE
Total calculations elapsed time: 3.01852297782898
Calculate GDI dataframe: DONE
Clean plots: START
Total calculations elapsed time: 0.0478439331054688
Clean plots: DONE
GDI plot
Removed 0 low GDI genes (such as the fully-expressed) in GDI plot
Cluster 2_4-merge, with size 430, is not uniform
Cluster 2_4-merge's shift to uniformity: 3.07228472969514
class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.397, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.583756345177665, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 3.7954982715656, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.407, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.576988155668359, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 4.08354952912925, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.5, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0.524534686971235, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 4.42722016730736, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.5, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 310, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 4.57228472969514, isUniform = FALSE, clusterSize = 430
Clusters 2 and 4 cannot be merged
Clusters 1 and 2 will be merged
Clusters 4 and 3 will be merged
Executed 2 merges
Loop calculations elapsed time: 16.9533607959747
Start merging nearest clusters: iteration 4
Differential Expression Analysis - START
* DEA on cluster '1_2-merge' with 499 cells
* DEA on cluster '3_4-merge' with 501 cells
Total calculations elapsed time: 0.0312378406524658
Differential Expression Analysis - DONE
Updating check results for the 3 already tested pairs to align to new checker
1 new clusters pairs to be tested for merging:
c("1_2-merge", "3_4-merge")
*1_2-merge_3_4-merge-merge
Asked to drop no genes or cells
COTAN dataset analysis: START
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [1000] cells
Dataset cleaning elapsed time: 1.84312081336975
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 7 iterations
Total calculations elapsed time: 4.07259678840637
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.0529252975916502 | max: 462.908586418991 | % negative: 17.3333333333333
Model parameter estimation elapsed time: 4.89414620399475
COTAN genes' COEX estimation: START
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not available yet
Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 3.25610709190369
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.0178639888763428
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.103567838668823
Estimating genes' COEX
Calculate genes' COEX elapsed time: 1.04517006874084
Total calculations elapsed time: 4.4227089881897
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 5.44638586044312
Dataset analysis elapsed time: 12.1836528778076
COTAN dataset analysis: DONE
Checking uniformity for the cluster '1_2-merge_3_4-merge-merge' with 1000 cells
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Total calculations elapsed time: 0.0314640998840332
Calculate `GDI`: DONE
Total calculations elapsed time: 2.99699711799622
Calculate GDI dataframe: DONE
Clean plots: START
Total calculations elapsed time: 0.0442719459533691
Clean plots: DONE
GDI plot
Removed 0 low GDI genes (such as the fully-expressed) in GDI plot
Cluster 1_2-merge_3_4-merge-merge, with size 1000, is not uniform
Cluster 1_2-merge_3_4-merge-merge's shift to uniformity: 3.86988385120409
class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.397, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.69, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 4.54596809454193, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.407, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.678333333333333, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 4.93144728766684, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.5, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0.593333333333333, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 5.2532296852478, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.5, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 356, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 5.36988385120409, isUniform = FALSE, clusterSize = 1000
Clusters 1_2-merge and 3_4-merge cannot be merged
No clusters will be merged
None of the remaining tested cluster pairs could be merged
Executed all merges for threshold 1.397 out of 4 checks
The final merged clusterization contains [2] different clusters: 1_2-merge, 3_4-merge
Differential Expression Analysis - START
* DEA on cluster '1' with 499 cells
* DEA on cluster '2' with 501 cells
Total calculations elapsed time: 0.0345590114593506
Differential Expression Analysis - DONE
Applied reordering to clusterization is:
1 -> 1, 2 -> 2
Total calculations elapsed time: 69.9926159381866
Merging cells' uniform clustering: DONE
Applied reordering to clusterization is:
1 -> 1, 2 -> 2
Log Fold Change Analysis - START
* Analysis of cluster: '1'
* Analysis of cluster: '2'
Total calculations elapsed time: 1.87558221817017
Log Fold Change Analysis - DONE
[1] "Tested cluster: 1"
Asked to drop 0 genes and 501 cells
COTAN dataset analysis: START
Asked to drop 16 genes and 0 cells
Genes/cells selection done: dropped [16] genes and [0] cells
Working on [584] genes and [499] cells
Dataset cleaning elapsed time: 0.993963003158569
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 10 iterations
Total calculations elapsed time: 1.98517608642578
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.0608154544840047 | max: 1260.06995351592 | % negative: 35.6164383561644
Model parameter estimation elapsed time: 2.94046902656555
COTAN genes' COEX estimation: START
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not available yet
Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 3.12235593795776
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.00928401947021484
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0361230373382568
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.944178104400635
Total calculations elapsed time: 4.11194109916687
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 5.06874704360962
Dataset analysis elapsed time: 9.00317907333374
COTAN dataset analysis: DONE
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Total calculations elapsed time: 0.0298118591308594
Calculate `GDI`: DONE
Total calculations elapsed time: 4.24672913551331
Calculate GDI dataframe: DONE
Dispersion bisection: straddling used 2 iterations
Dispersion bisection: used 8 iterations
Dispersion bisection: straddling used 1 iterations
Dispersion bisection: used 9 iterations
Dispersion Newton-Raphson: used up to 4 iterations
Dispersion Newton-Raphson: used up to 4 iterations
parallel dispersion bisection: straddling used up to 2 iterations
Parallel dispersion bisection: used up to 9 iterations
Parallel dispersion Newton-Raphson: used up to 4 iterations
[ FAIL 0 | WARN 3 | SKIP 0 | PASS 572 ]
[ FAIL 0 | WARN 3 | SKIP 0 | PASS 572 ]
>
> proc.time()
user system elapsed
699.698 10.421 718.457
COTAN.Rcheck/COTAN-Ex.timings
| name | user | system | elapsed | |
| COTAN_Legacy | 0.002 | 0.000 | 0.002 | |
| COTAN_ObjectCreation | 11.494 | 0.281 | 11.842 | |
| CalculatingCOEX | 52.940 | 0.987 | 54.213 | |
| ClustersList | 0.010 | 0.002 | 0.012 | |
| Conversions | 4.909 | 0.114 | 5.044 | |
| GenesStatistics | 10.609 | 0.384 | 10.881 | |
| HandleMetaData | 0.041 | 0.003 | 0.044 | |
| HandlingClusterizations | 41.858 | 1.055 | 42.730 | |
| HandlingConditions | 0.075 | 0.004 | 0.080 | |
| HeatmapPlots | 31.107 | 0.830 | 32.184 | |
| Installing_torch | 0 | 0 | 0 | |
| LoggingFunctions | 0.002 | 0.001 | 0.004 | |
| ParametersEstimations | 21.679 | 0.645 | 22.498 | |
| RawDataCleaning | 4.700 | 0.306 | 4.818 | |
| RawDataGetters | 0.030 | 0.004 | 0.034 | |
| UniformClusters | 66.103 | 1.676 | 67.193 | |
| getColorsVector | 0.001 | 0.014 | 0.001 | |