Galfrè Silvia Giulia
| Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024) |
| git_url: https://git.bioconductor.org/packages/COTAN |
| git_branch: devel |
| git_last_commit: 2600866 |
| git_last_commit_date: 2024-06-03 17:30:58 -0400 (Mon, 03 Jun 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-06-11 15:41 -0400 (Tue, 11 Jun 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4679 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4414 |
| merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4441 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4394 |
| 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 435/2239 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| COTAN 2.5.2 (landing page) Galfrè Silvia Giulia
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | 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: 2.5.2 |
| 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_2.5.2.tar.gz |
| StartedAt: 2024-06-10 01:50:54 -0400 (Mon, 10 Jun 2024) |
| EndedAt: 2024-06-10 02:20:18 -0400 (Mon, 10 Jun 2024) |
| EllapsedTime: 1764.0 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_2.5.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/COTAN.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘COTAN/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘COTAN’ version ‘2.5.2’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 dependencies in R code ... NOTE
'library' or 'require' call to ‘torch’ in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Unexported object imported by a ':::' call: ‘ggplot2:::ggname’
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
GDIPlot: no visible binding for global variable ‘sum.raw.norm’
GDIPlot: no visible binding for global variable ‘GDI’
UMAPPlot: no visible binding for global variable ‘x’
UMAPPlot: no visible binding for global variable ‘y’
calculateCoex_Legacy: no visible binding for global variable
‘expectedNN’
calculateCoex_Legacy: no visible binding for global variable
‘expectedNY’
calculateCoex_Legacy: no visible binding for global variable
‘expectedYN’
calculateCoex_Legacy: no visible binding for global variable
‘expectedYY’
calculateCoex_Legacy: no visible binding for global variable
‘observedYY’
calculateCoex_Legacy: no visible binding for global variable ‘.’
calculateG: no visible binding for global variable ‘observedNN’
calculateG: no visible binding for global variable ‘observedNY’
calculateG: no visible binding for global variable ‘observedYN’
calculateG: no visible binding for global variable ‘observedYY’
calculateG: no visible binding for global variable ‘expectedNN’
calculateG: no visible binding for global variable ‘expectedNY’
calculateG: no visible binding for global variable ‘expectedYN’
calculateG: no visible binding for global variable ‘expectedYY’
calculatePartialCoex: no visible binding for global variable
‘expectedNN’
calculatePartialCoex: no visible binding for global variable
‘expectedNY’
calculatePartialCoex: no visible binding for global variable
‘expectedYN’
calculatePartialCoex: no visible binding for global variable
‘expectedYY’
calculatePartialCoex: no visible binding for global variable
‘observedYY’
calculatePartialCoex: no visible binding for global variable ‘.’
cellsUniformClustering: no visible binding for global variable
‘objSeurat’
cellsUniformClustering: no visible binding for global variable
‘usedMaxResolution’
cellsUniformClustering: no visible binding for global variable
‘permMap’
checkClusterUniformity: ... may be used in an incorrect context:
‘c(..., nuPlot, zoomedNuPlot)’
checkClusterUniformity: no visible binding for global variable ‘nuPlot’
checkClusterUniformity: no visible binding for global variable
‘zoomedNuPlot’
cleanPlots: no visible binding for global variable ‘PC1’
cleanPlots: no visible binding for global variable ‘PC2’
cleanPlots: no visible binding for global variable ‘n’
cleanPlots: no visible binding for global variable ‘means’
cleanPlots: no visible binding for global variable ‘nu’
clustersMarkersHeatmapPlot: no visible binding for global variable
‘condName’
clustersMarkersHeatmapPlot: no visible binding for global variable
‘conditions’
clustersSummaryPlot: no visible binding for global variable ‘keys’
clustersSummaryPlot: no visible binding for global variable ‘values’
clustersSummaryPlot: no visible binding for global variable
‘CellNumber’
clustersSummaryPlot: no visible binding for global variable ‘ExpGenes’
clustersSummaryPlot: no visible binding for global variable ‘Cluster’
clustersSummaryPlot: no visible binding for global variable ‘Condition’
establishGenesClusters: no visible binding for global variable
‘secondaryMarkers’
establishGenesClusters: no visible binding for global variable ‘GCS’
establishGenesClusters: no visible binding for global variable
‘rankGenes’
expectedContingencyTables: no visible binding for global variable
‘expectedN’
expectedPartialContingencyTables: no visible binding for global
variable ‘expectedNN’
expectedPartialContingencyTables: no visible binding for global
variable ‘expectedN’
geom_flat_violin : <anonymous>: no visible binding for global variable
‘group’
geom_flat_violin : <anonymous>: no visible binding for global variable
‘y’
geom_flat_violin : <anonymous>: no visible binding for global variable
‘x’
geom_flat_violin : <anonymous>: no visible binding for global variable
‘width’
geom_flat_violin : <anonymous>: no visible binding for global variable
‘violinwidth’
geom_flat_violin : <anonymous>: no visible binding for global variable
‘xmax’
geom_flat_violin : <anonymous>: no visible binding for global variable
‘xminv’
geom_flat_violin : <anonymous>: no visible binding for global variable
‘xmaxv’
heatmapPlot: no visible binding for global variable ‘g2’
mergeUniformCellsClusters : testPairListMerge: no visible binding for
global variable ‘cl1’
mergeUniformCellsClusters : testPairListMerge: no visible binding for
global variable ‘cl2’
mergeUniformCellsClusters: no visible binding for global variable
‘permMap’
mitochondrialPercentagePlot: no visible binding for global variable
‘mit.percentage’
observedContingencyTables: no visible binding for global variable
‘observedY’
observedPartialContingencyTables: no visible binding for global
variable ‘observedYY’
observedPartialContingencyTables: no visible binding for global
variable ‘observedY’
scatterPlot: no visible binding for global variable ‘.x’
calculateCoex,COTAN: no visible binding for global variable ‘useTorch’
coerce,COTAN-scCOTAN: no visible binding for global variable ‘rawNorm’
coerce,COTAN-scCOTAN: no visible binding for global variable ‘nu’
coerce,COTAN-scCOTAN: no visible binding for global variable ‘lambda’
coerce,COTAN-scCOTAN: no visible binding for global variable ‘a’
coerce,COTAN-scCOTAN: no visible binding for global variable ‘hk’
coerce,COTAN-scCOTAN: no visible binding for global variable ‘clusters’
coerce,COTAN-scCOTAN: no visible binding for global variable
‘clusterData’
Undefined global functions or variables:
. .x CellNumber Cluster Condition ExpGenes GCS GDI PC1 PC2 a cl1 cl2
clusterData clusters condName conditions expectedN expectedNN
expectedNY expectedYN expectedYY g2 group hk keys lambda means
mit.percentage n nu nuPlot objSeurat observedNN observedNY observedY
observedYN observedYY permMap rankGenes rawNorm secondaryMarkers
sum.raw.norm useTorch usedMaxResolution values violinwidth width x
xmax xmaxv xminv y zoomedNuPlot
* 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 166.538 1.709 191.778
HeatmapPlots 61.153 2.003 74.007
CalculatingCOEX 61.521 1.159 72.144
HandlingClusterizations 35.538 0.831 43.548
ParametersEstimations 32.748 0.808 39.013
GenesStatistics 11.689 0.219 14.129
COTANObjectCreation 11.201 0.377 12.959
RawDataCleaning 10.727 0.349 12.675
* 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: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.20-bioc/meat/COTAN.Rcheck/00check.log’
for details.
COTAN.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL COTAN ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘COTAN’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading Note: ... may be used in an incorrect context ** 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 version 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup"
Copyright (C) 2024 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
> library(zeallot)
>
> outputTestDatasetCreation <- function(testsDir = file.path("tests",
+ "testthat")) {
+ utils::data("test.dataset", package = "COTAN")
+ options(parallelly.fork.enable = TRUE)
+
+ obj <- COTAN(raw = test.dataset)
+ obj <- initializeMetaDataset(obj, GEO = " ",
+ sequencingMethod = "artificial",
+ sampleCondition = "test")
+
+ obj <- proceedToCoex(obj, cores = 6L, saveObj = FALSE)
+ #saveRDS(obj, file = file.path(testsDir,"temp.RDS"))
+
+ cells.names.test <- getCells(obj)[c(1L:10L, 591L:610L, 991L:1000L)]
+ genes.names.test <- getGenes(obj)[c(1L:10L, 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"))
+
+ dispersion.test <- getDispersion(obj)[genes.names.test]
+ saveRDS(dispersion.test, file.path(testsDir, "dispersion.test.RDS"))
+
+ raw.norm.test <- getNormalizedData(obj)[genes.names.test, cells.names.test]
+ saveRDS(raw.norm.test, file.path(testsDir, "raw.norm.test.RDS"))
+
+ coex.test <- getGenesCoex(obj, genes = genes.names.test, zeroDiagonal = FALSE)
+ saveRDS(coex.test, file.path(testsDir, "coex.test.RDS"))
+
+ lambda.test <- getLambda(obj)[genes.names.test]
+ saveRDS(lambda.test, file.path(testsDir, "lambda.test.RDS"))
+
+ GDI.test <- calculateGDI(obj)
+ GDI.test <- GDI.test[genes.names.test, ]
+ saveRDS(GDI.test, file.path(testsDir, "GDI.test.RDS"))
+
+ nu.test <- getNu(obj)[cells.names.test]
+ saveRDS(nu.test, file.path(testsDir, "nu.test.RDS"))
+
+ pval.test <- calculatePValue(obj, geneSubsetCol = genes.names.test)
+ saveRDS(pval.test, file.path(testsDir, "pval.test.RDS"))
+
+ GDIThreshold <- 1.46
+ initialResolution <- 0.8
+
+ clusters <- cellsUniformClustering(obj, GDIThreshold = GDIThreshold,
+ initialResolution = initialResolution,
+ cores = 6L, saveObj = FALSE)[["clusters"]]
+ saveRDS(clusters, file.path(testsDir, "clusters1.RDS"))
+
+ coexDF <- DEAOnClusters(obj, clusters = clusters)
+ obj <- addClusterization(obj, clName = "clusters",
+ clusters = clusters, coexDF = coexDF)
+
+ saveRDS(coexDF[genes.names.test, ],
+ file.path(testsDir, "coex.test.cluster1.RDS"))
+
+ pvalDF <- pValueFromDEA(coexDF, getNumCells(obj), method = "none")
+
+ saveRDS(pvalDF[genes.names.test, ],
+ file.path(testsDir, "pval.test.cluster1.RDS"))
+
+ c(mergedClusters, mCoexDF) %<-%
+ mergeUniformCellsClusters(objCOTAN = obj,
+ clusters = NULL,
+ GDIThreshold = GDIThreshold,
+ cores = 6L,
+ distance = "cosine",
+ hclustMethod = "ward.D2",
+ saveObj = FALSE)
+
+ saveRDS(mergedClusters[genes.names.test],
+ file.path(testsDir, "cluster_data_merged.RDS"))
+ }
>
> proc.time()
user system elapsed
0.395 0.123 0.508
COTAN.Rcheck/tests/spelling.Rout
R version 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup"
Copyright (C) 2024 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)
NULL
>
> proc.time()
user system elapsed
0.371 0.121 0.489
COTAN.Rcheck/tests/testthat.Rout
R version 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup"
Copyright (C) 2024 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)
> 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 from [1:10] to [1:10]
Estimate dispersion: DONE
dispersion | min: 0.9033203125 | max: 4.6796875 | % 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: 2.76803278923035
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.00244903564453125
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0168020725250244
Estimating genes' coex
Calculate genes' coex elapsed time: 0.942470073699951
Total calculations elapsed time: 3.72975397109985
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 4 genes batches from [1:2] to [7:8]
Executing 1 genes batches from [9:10] to [9:10]
Estimate dispersion: DONE
dispersion | min: 0.9033203125 | max: 4.6796875 | % negative: 10
Estimate nu: START
Effective number of cores used: 1
Executing 4 cells batches from [1:3] to [10:11]
Executing 3 cells batches from [12:14] to [18:20]
Estimate nu: DONE
nu change (abs) | max: 1.75595238095238 | median: 1.07174634176587 | mean: 1.07174634176587
Estimate 'dispersion'/'nu': START
Estimate dispersion: START
Effective number of cores used: 1
Executing 1 genes batches from [1:10] to [1:10]
Estimate dispersion: DONE
dispersion | min: 1.0362548828125 | max: 4.60986328125 | % negative: 10
Estimate nu: START
Effective number of cores used: 1
Executing 1 cells batches from [1:20] to [1:20]
Estimate nu: DONE
nu change (abs) | max: 0.0265938895089288 | median: 0.0144680038331048 | mean: 0.0144680038331048
Nu mean: 1.69633192486233
Marginal errors | max: 1.95570586131367 | median 1.32068160171502 | mean: 1.33375826507259
Estimate dispersion: START
Effective number of cores used: 1
Executing 1 genes batches from [1:10] to [1:10]
Estimate dispersion: DONE
dispersion | min: 0.058837890625 | max: 3.528076171875 | % negative: 10
Estimate nu: START
Effective number of cores used: 1
Executing 1 cells batches from [1:20] to [1:20]
Estimate nu: DONE
nu change (abs) | max: 0.416683423613994 | median: 0.239880630367975 | mean: 0.239880630367975
Nu mean: 0.823197206753982
Marginal errors | max: 0.836359531101206 | median 0.703684202571891 | mean: 0.645537958989614
Estimate dispersion: START
Effective number of cores used: 1
Executing 1 genes batches from [1:10] to [1:10]
Estimate dispersion: DONE
dispersion | min: 0.32879638671875 | max: 4.0302734375 | % negative: 10
Estimate nu: START
Effective number of cores used: 1
Executing 1 cells batches from [1:20] to [1:20]
Estimate nu: DONE
nu change (abs) | max: 0.164237872898673 | median: 0.0955985184389135 | mean: 0.0955985184389135
Nu mean: 1.06863935445976
Marginal errors | max: 0.259872988828242 | median 0.213703042752633 | mean: 0.197386407582083
Estimate dispersion: START
Effective number of cores used: 1
Executing 1 genes batches from [1:10] to [1:10]
Estimate dispersion: DONE
dispersion | min: 0.2294921875 | max: 3.8720703125 | % negative: 10
Estimate nu: START
Effective number of cores used: 1
Executing 1 cells batches from [1:20] to [1:20]
Estimate nu: DONE
nu change (abs) | max: 0.055185575120883 | median: 0.0319991762044448 | mean: 0.0319991762044448
Nu mean: 0.976813601083562
Marginal errors | max: 0.0951586919577032 | median 0.079429703709466 | mean: 0.0724140148396648
Estimate dispersion: START
Effective number of cores used: 1
Executing 1 genes batches from [1:10] to [1:10]
Estimate dispersion: DONE
dispersion | min: 0.2637939453125 | max: 3.929443359375 | % negative: 10
Estimate nu: START
Effective number of cores used: 1
Executing 1 cells batches from [1:20] to [1:20]
Estimate nu: DONE
nu change (abs) | max: 0.0196211148938294 | median: 0.01138609597457 | mean: 0.01138609597457
Nu mean: 1.00823501891926
Marginal errors | max: 0.0327747321002292 | median 0.0272104747849538 | mean: 0.0248963830312038
Estimate dispersion: START
Effective number of cores used: 1
Executing 1 genes batches from [1:10] to [1:10]
Estimate dispersion: DONE
dispersion | min: 0.25177001953125 | max: 3.90966796875 | % negative: 10
Estimate nu: START
Effective number of cores used: 1
Executing 1 cells batches from [1:20] to [1:20]
Estimate nu: DONE
nu change (abs) | max: 0.00670099066960717 | median: 0.00388888266671264 | mean: 0.00388888266671264
Nu mean: 0.997187891997105
Marginal errors | max: 0.0114324509186883 | median 0.0094232649770607 | mean: 0.00863113610779571
Estimate dispersion: START
Effective number of cores used: 1
Executing 1 genes batches from [1:10] to [1:10]
Estimate dispersion: DONE
dispersion | min: 0.25592041015625 | max: 3.91650390625 | % negative: 10
Estimate nu: START
Effective number of cores used: 1
Executing 1 cells batches from [1:20] to [1:20]
Estimate nu: DONE
nu change (abs) | max: 0.00230093811689414 | median: 0.00132529122122246 | mean: 0.00132529122122246
Nu mean: 1.00097564689567
Marginal errors | max: 0.00387133150664631 | median 0.0031091017608853 | mean: 0.00286071175800213
Estimate dispersion: START
Effective number of cores used: 1
Executing 1 genes batches from [1:10] to [1:10]
Estimate dispersion: DONE
dispersion | min: 0.2545166015625 | max: 3.914306640625 | % negative: 10
Estimate nu: START
Effective number of cores used: 1
Executing 1 cells batches from [1:20] to [1:20]
Estimate nu: DONE
nu change (abs) | max: 0.000837011646904529 | median: 0.000470837393363011 | mean: 0.000470837393363011
Nu mean: 0.999633825746458
Marginal errors | max: 0.00122501723202006 | median 0.00102126435760308 | mean: 0.000943992659051318
Estimate dispersion: START
Effective number of cores used: 1
Executing 1 genes batches from [1:10] to [1:10]
Estimate dispersion: DONE
dispersion | min: 0.2550048828125 | max: 3.9150390625 | % negative: 10
Estimate nu: START
Effective number of cores used: 1
Executing 1 cells batches from [1:20] to [1:20]
Estimate nu: DONE
nu change (abs) | max: 0.000209227351122054 | median: 0.000122070312500028 | mean: 0.000122070312500028
Nu mean: 1.00008715703862
Marginal errors | max: 0.000364602956581805 | median 0.000313956936819793 | mean: 0.000282899574318485
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 from [1:10] to [1:10]
Estimate dispersion: DONE
dispersion | min: 0.9033203125 | max: 4.6796875 | % 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 avalable 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: 2.87441992759705
Calculating genes' coex normalization factor
Fraction of genes' with very low expected contingency tables: 0.181818181818182
Calculate genes' normalization factor elapsed time: 0.00177693367004395
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.00781607627868652
Estimating genes' coex
Calculate genes' coex elapsed time: 0.949250936508179
Total calculations elapsed time: 3.83326387405396
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: 2.85973906517029
Calculating cells' coex normalization factor
Fraction of cells' with very low expected contingency tables: 0
Calculate cells' normalization factor elapsed time: 0.00170493125915527
Retrieving observed cells' yes/yes contingency table
calculating YY.. done
Observed cells' contingency table elapsed time: 0.0049591064453125
Estimating cells' coex
Calculate cells' coex elapsed time: 0.976200819015503
Total calculations elapsed time: 3.84260392189026
Calculate cells' coex (legacy): 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 from [1:10] to [1:10]
Estimate dispersion: DONE
dispersion | min: 0.903564453125 | max: 4.679443359375 | % negative: 10
Estimate nu: START
Effective number of cores used: 1
Executing 1 cells batches from [1:20] to [1:20]
Estimate nu: DONE
nu change (abs) | max: 1.75719246031746 | median: 1.07229953342014 | mean: 1.07229953342014
Nu mean: 1.68489292689732
Marginal errors | max: 1.73564890252257 | median 1.37996360874076 | mean: 1.32180348113228
Estimate dispersion: START
Effective number of cores used: 1
Executing 1 genes batches from [1:10] to [1:10]
Estimate dispersion: DONE
dispersion | min: 0.0655517578125 | max: 3.5439453125 | % negative: 10
Estimate nu: START
Effective number of cores used: 1
Executing 1 cells batches from [1:20] to [1:20]
Estimate nu: DONE
nu change (abs) | max: 0.402649984216273 | median: 0.231868788425666 | mean: 0.231868788425666
Nu mean: 0.829218804209393
Marginal errors | max: 0.80321315986594 | median 0.677497553540581 | mean: 0.619375430892821
Estimate dispersion: START
Effective number of cores used: 1
Executing 1 genes batches from [1:10] to [1:10]
Estimate dispersion: DONE
dispersion | min: 0.3260498046875 | max: 4.026123046875 | % negative: 10
Estimate nu: START
Effective number of cores used: 1
Executing 1 cells batches from [1:20] to [1:20]
Estimate nu: DONE
nu change (abs) | max: 0.158004893526231 | median: 0.0919692884670312 | mean: 0.0919692884670312
Nu mean: 1.0660356050592
Marginal errors | max: 0.250724014302326 | median 0.206232152124436 | mean: 0.190425623677198
Estimate dispersion: START
Effective number of cores used: 1
Executing 1 genes batches from [1:10] to [1:10]
Estimate dispersion: DONE
dispersion | min: 0.23040771484375 | max: 3.8736572265625 | % negative: 10
Estimate nu: START
Effective number of cores used: 1
Executing 1 cells batches from [1:20] to [1:20]
Estimate nu: DONE
nu change (abs) | max: 0.0532774732102337 | median: 0.0308837890624999 | mean: 0.0308837890624999
Nu mean: 0.977606315852266
Marginal errors | max: 0.0916983669060123 | median 0.0765266929824948 | mean: 0.0697593208689684
Estimate dispersion: START
Effective number of cores used: 1
Executing 1 genes batches from [1:10] to [1:10]
Estimate dispersion: DONE
dispersion | min: 0.26348876953125 | max: 3.928955078125 | % negative: 10
Estimate nu: START
Effective number of cores used: 1
Executing 1 cells batches from [1:20] to [1:20]
Estimate nu: DONE
nu change (abs) | max: 0.0189966206463044 | median: 0.0110199320575908 | mean: 0.0110199320575908
Nu mean: 1.00797668858871
Marginal errors | max: 0.0317151207459254 | median 0.0262702142278251 | mean: 0.0240886952086962
Estimate dispersion: START
Effective number of cores used: 1
Executing 1 genes batches from [1:10] to [1:10]
Estimate dispersion: DONE
dispersion | min: 0.2518310546875 | max: 3.9097900390625 | % negative: 10
Estimate nu: START
Effective number of cores used: 1
Executing 1 cells batches from [1:20] to [1:20]
Estimate nu: DONE
nu change (abs) | max: 0.00670088501353994 | median: 0.00388888101583662 | mean: 0.00388888101583662
Nu mean: 0.997187996002297
Marginal errors | max: 0.0113693316356223 | median 0.00939669372836249 | mean: 0.00860715734056932
Estimate dispersion: START
Effective number of cores used: 1
Executing 1 genes batches from [1:10] to [1:10]
Estimate dispersion: DONE
dispersion | min: 0.2559814453125 | max: 3.9166259765625 | % negative: 10
Estimate nu: START
Effective number of cores used: 1
Executing 1 cells batches from [1:20] to [1:20]
Estimate nu: DONE
nu change (abs) | max: 0.00251007446998996 | median: 0.00144735987374958 | mean: 0.00144735987374958
Nu mean: 1.00106271459624
Marginal errors | max: 0.00406746973787442 | median 0.00343393462175534 | mean: 0.00313496757119527
Estimate dispersion: START
Effective number of cores used: 1
Executing 1 genes batches from [1:10] to [1:10]
Estimate dispersion: DONE
dispersion | min: 0.25445556640625 | max: 3.9140625 | % negative: 10
Estimate nu: START
Effective number of cores used: 1
Executing 1 cells batches from [1:20] to [1:20]
Estimate nu: DONE
nu change (abs) | max: 0.000837027590858019 | median: 0.000488281249999889 | mean: 0.000488281249999889
Nu mean: 0.999651253659142
Marginal errors | max: 0.00143433714371533 | median 0.00116636244706747 | mean: 0.00109289166947839
Estimate dispersion: START
Effective number of cores used: 1
Executing 1 genes batches from [1:10] to [1:10]
Estimate dispersion: DONE
dispersion | min: 0.2550048828125 | max: 3.9150390625 | % negative: 10
Estimate nu: START
Effective number of cores used: 1
Executing 1 cells batches from [1:20] to [1:20]
Estimate nu: DONE
nu change (abs) | max: 0.000209227688885871 | median: 0.0001220703125 | mean: 0.0001220703125
Nu mean: 1.00008715737639
Marginal errors | max: 0.000379524846207957 | median 0.000325685250686547 | mean: 0.000295532844332236
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 avalable 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: 2.75138211250305
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.00131797790527344
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.00739192962646484
Estimating genes' coex
Calculate genes' coex elapsed time: 0.918951034545898
Total calculations elapsed time: 3.67904305458069
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: 2.75323295593262
Calculating cells' coex normalization factor
Calculate cells' normalization factor elapsed time: 0.0013740062713623
Retrieving observed cells' yes/yes contingency table
calculating YY.. done
Observed cells' contingency table elapsed time: 0.00465106964111328
Estimating cells' coex
Calculate cells' coex elapsed time: 0.920853853225708
Total calculations elapsed time: 3.6801118850708
Calculate cells' 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: 0.325
Retrieving observed genes' yes/yes partial contingency table
calculating partial YY.. done
Estimating genes' partial coex
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
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
Attaching package: 'rlang'
The following objects are masked from 'package:testthat':
is_false, is_null, is_true
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 from [1:3] to [8:10]
Estimate dispersion: DONE
dispersion | min: 0.9033203125 | max: 4.6796875 | % 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: 2.80037117004395
Calculating genes' coex normalization factor
Fraction of genes' with very low expected contingency tables: 0.181818181818182
Calculate genes' normalization factor elapsed time: 0.00174093246459961
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0048830509185791
Estimating genes' coex
Calculate genes' coex elapsed time: 0.915313005447388
Total calculations elapsed time: 3.72230815887451
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 avalable 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: 2.86092901229858
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.00134706497192383
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.00399899482727051
Estimating genes' coex
Calculate genes' coex elapsed time: 0.91559886932373
Total calculations elapsed time: 3.78187394142151
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
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
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 from [1:3] to [8:10]
Estimate dispersion: DONE
dispersion | min: 0.903564453125 | max: 4.679443359375 | % negative: 10
Estimate nu: START
Effective number of cores used: 1
Executing 4 cells batches from [1:4] to [13:16]
Executing 1 cells batches from [17:20] to [17:20]
Estimate nu: DONE
nu change (abs) | max: 1.75719246031746 | median: 1.07229953342014 | mean: 1.07229953342014
Nu mean: 1.68489292689732
Marginal errors | max: 0.25535328937316 | median 0.0807577993228135 | mean: 0.101980750205762
Estimate dispersion: START
Effective number of cores used: 1
Executing 3 genes batches from [1:3] to [8:10]
Estimate dispersion: DONE
dispersion | min: 1.037109375 | max: 4.6107177734375 | % negative: 10
Estimate nu: START
Effective number of cores used: 1
Executing 4 cells batches from [1:4] to [13:16]
Executing 1 cells batches from [17:20] to [17:20]
Estimate nu: DONE
nu change (abs) | max: 0.0273438105507502 | median: 0.0148852611818011 | mean: 0.0148852611818011
Nu mean: 1.69735147626627
Marginal errors | max: 0.00326864580272002 | median 0.00111524657842743 | mean: 0.00131556083122533
Estimate dispersion: START
Effective number of cores used: 1
Executing 3 genes batches from [1:3] to [8:10]
Estimate dispersion: DONE
dispersion | min: 1.03887939453125 | max: 4.6097412109375 | % negative: 10
Estimate nu: START
Effective number of cores used: 1
Executing 4 cells batches from [1:4] to [13:16]
Executing 1 cells batches from [17:20] to [17:20]
Estimate nu: DONE
nu change (abs) | max: 0 | median: 0 | mean: 0
Nu mean: 1.69735147626627
Marginal errors | max: 7.56328383637594e-05 | median 1.72948087246994e-05 | mean: 2.99252342145451e-05
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: 3.07681202888489
Calculating cells' coex normalization factor
Fraction of cells' with very low expected contingency tables: 0
Calculate cells' normalization factor elapsed time: 0.00364398956298828
Retrieving observed cells' yes/yes contingency table
calculating YY.. done
Observed cells' contingency table elapsed time: 0.00754690170288086
Estimating cells' coex
Calculate cells' coex elapsed time: 0.987473011016846
Total calculations elapsed time: 4.0754759311676
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
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
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 from [1:3] to [8:10]
Estimate dispersion: DONE
dispersion | min: 0.903564453125 | max: 4.679443359375 | % negative: 10
Estimate nu: START
Effective number of cores used: 1
Executing 4 cells batches from [1:4] to [13:16]
Executing 1 cells batches from [17:20] to [17:20]
Estimate nu: DONE
nu change (abs) | max: 1.75719246031746 | median: 1.07229953342014 | mean: 1.07229953342014
Nu mean: 1.68489292689732
Marginal errors | max: 0.25535328937316 | median 0.0807577993228135 | mean: 0.101980750205762
Estimate dispersion: START
Effective number of cores used: 1
Executing 3 genes batches from [1:3] to [8:10]
Estimate dispersion: DONE
dispersion | min: 1.037109375 | max: 4.6107177734375 | % negative: 10
Estimate nu: START
Effective number of cores used: 1
Executing 4 cells batches from [1:4] to [13:16]
Executing 1 cells batches from [17:20] to [17:20]
Estimate nu: DONE
nu change (abs) | max: 0.0273438105507502 | median: 0.0148852611818011 | mean: 0.0148852611818011
Nu mean: 1.69735147626627
Marginal errors | max: 0.00326864580272002 | median 0.00111524657842743 | mean: 0.00131556083122533
Estimate dispersion: START
Effective number of cores used: 1
Executing 3 genes batches from [1:3] to [8:10]
Estimate dispersion: DONE
dispersion | min: 1.03887939453125 | max: 4.6097412109375 | % negative: 10
Estimate nu: START
Effective number of cores used: 1
Executing 4 cells batches from [1:4] to [13:16]
Executing 1 cells batches from [17:20] to [17:20]
Estimate nu: DONE
nu change (abs) | max: 0 | median: 0 | mean: 0
Nu mean: 1.69735147626627
Marginal errors | max: 7.56328383637594e-05 | median 1.72948087246994e-05 | mean: 2.99252342145451e-05
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: 2.60634803771973
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.00129103660583496
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.00377297401428223
Estimating genes' coex
Calculate genes' coex elapsed time: 0.906475067138672
Total calculations elapsed time: 3.51788711547852
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
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
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
Calculating G: DONE
calculating PValues: START
Get p-values on a set of genes on columns and on a set of genes on rows
calculating PValues: DONE
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
S matrix sorted
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
Calculating G: DONE
S matrix sorted
Calculate GDI dataframe: DONE
Calculating S: START
Calculating S: DONE
S matrix sorted
S matrix sorted
Initializing `COTAN` meta-data
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [1200] cells
Estimate dispersion: START
Effective number of cores used: 1
Executing 1 genes batches from [1:600] to [1:600]
Estimate dispersion: DONE
dispersion | min: 0.2197265625 | max: 6.08056640625 | % negative: 0
Only analysis elapsed time: 4.26303291320801
Cotan genes' coex estimation started
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: 3.50056004524231
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.0159070491790771
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0622928142547607
Estimating genes' coex
Calculate genes' coex elapsed time: 0.974022150039673
Total calculations elapsed time: 4.55278205871582
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 5.5263090133667
Total elapsed time: 10.7096109390259
Initializing `COTAN` meta-data
Condition test
n cells 1200
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [1200] cells
Estimate dispersion: START
Effective number of cores used: 1
Executing 1 genes batches from [1:600] to [1:600]
Estimate dispersion: DONE
dispersion | min: 0.2197265625 | max: 6.08056640625 | % negative: 0
Only analysis elapsed time: 4.183837890625
Cotan genes' coex estimation started
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: 3.63359904289246
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.0164039134979248
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0636498928070068
Estimating genes' coex
Calculate genes' coex elapsed time: 0.951572179794312
Total calculations elapsed time: 4.6652250289917
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 5.60041093826294
Total elapsed time: 10.7170009613037
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
calculating PValues: DONE
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
S matrix sorted
Calculate GDI dataframe: DONE
Initializing `COTAN` meta-data
Condition test
n cells 1200
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [1200] cells
Estimate dispersion: START
Effective number of cores used: 1
Executing 1 genes batches from [1:600] to [1:600]
Estimate dispersion: DONE
dispersion | min: 0.2197265625 | max: 6.08056640625 | % negative: 0
Only analysis elapsed time: 4.03296589851379
Cotan genes' coex estimation started
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 avalable 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: 3.73367500305176
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.0124449729919434
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0612421035766602
Estimating genes' coex
Calculate genes' coex elapsed time: 0.933584928512573
Total calculations elapsed time: 4.74094700813293
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 5.66788792610168
Total elapsed time: 10.6344339847565
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
calculating PValues: DONE
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
S matrix sorted
Calculate GDI dataframe: DONE
Initializing `COTAN` meta-data
Condition test
n cells 1200
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [1200] cells
Estimate dispersion: START
Effective number of cores used: 1
Executing 1 genes batches from [1:600] to [1:600]
Estimate dispersion: DONE
dispersion | min: 0.2197265625 | max: 6.08056640625 | % negative: 0
Only analysis elapsed time: 4.36175584793091
Cotan genes' coex estimation started
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 avalable 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: 3.72181510925293
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.0146110057830811
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0620880126953125
Estimating genes' coex
Calculate genes' coex elapsed time: 0.950722932815552
Total calculations elapsed time: 4.74923706054688
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 5.78114295005798
Total elapsed time: 11.090530872345
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
calculating PValues: DONE
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
S matrix sorted
Calculate GDI dataframe: DONE
Initializing `COTAN` meta-data
Asked to drop 0 genes and 1160 cells
Cotan analysis functions started
Asked to drop 31 genes and 0 cells
Genes/cells selection done: dropped [31] genes and [0] cells
Working on [569] genes and [40] cells
Estimate dispersion: START
Effective number of cores used: 1
Executing 1 genes batches from [1:569] to [1:569]
Estimate dispersion: DONE
dispersion | min: -0.2119140625 | max: 85.5 | % negative: 62.2144112478032
Cotan genes' coex estimation not requested
Total elapsed time: 4.67769384384155
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: 2.86496591567993
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.0118460655212402
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.00968289375305176
Estimating genes' coex
Calculate genes' coex elapsed time: 0.955435037612915
Total calculations elapsed time: 3.84192991256714
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 avalable 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: 2.92447209358215
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.0116441249847412
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0105838775634766
Estimating genes' coex
Calculate genes' coex elapsed time: 0.910254001617432
Total calculations elapsed time: 3.8569540977478
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 avalable 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: 2.93863105773926
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.011523962020874
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0130019187927246
Estimating genes' coex
Calculate genes' coex elapsed time: 0.97029709815979
Total calculations elapsed time: 3.93345403671265
Calculate genes' coex (legacy): DONE
Initializing `COTAN` meta-data
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [1200] cells
PCA: START
PCA: DONE
Hierarchical clustering: START
Hierarchical clustering: DONE
Estimate dispersion: START
Effective number of cores used: 1
Executing 1 genes batches from [1:600] to [1:600]
Estimate dispersion: DONE
dispersion | min: 0.2197265625 | max: 6.08056640625 | % negative: 0
Cotan genes' coex estimation not requested
Total elapsed time: 11.8249228000641
Saving elaborated data locally at: /tmp/Rtmpa9V7l9/test.cotan.RDS
Creating cells' uniform clustering: START
In iteration 1 the number of cells to re-cluster is 1200 cells belonging to 0 clusters
Creating Seurat object: 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%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Centering and scaling data matrix
|
| | 0%
|
|======================================================================| 100%
PC_ 1
Positive: g-000558, g-000570, g-000499, g-000504, g-000546, g-000506, g-000503, g-000517, g-000596, g-000528
g-000527, g-000580, g-000592, g-000578, g-000509, g-000488, g-000555, g-000577, g-000534, g-000583
g-000598, g-000535, g-000512, g-000554, g-000519, g-000525, g-000548, g-000544, g-000502, g-000541
Negative: g-000133, g-000007, g-000074, g-000141, g-000057, g-000235, g-000170, g-000019, g-000195, g-000140
g-000183, g-000031, g-000046, g-000178, g-000177, g-000161, g-000157, g-000139, g-000011, g-000135
g-000125, g-000208, g-000061, g-000085, g-000204, g-000104, g-000237, g-000004, g-000038, g-000128
PC_ 2
Positive: g-000039, g-000050, g-000175, g-000078, g-000116, g-000189, g-000135, g-000047, g-000072, g-000087
g-000063, g-000235, g-000066, g-000109, g-000018, g-000074, g-000231, g-000136, g-000034, g-000207
g-000128, g-000167, g-000171, g-000049, g-000182, g-000013, g-000054, g-000062, g-000240, g-000158
Negative: g-000584, g-000583, g-000544, g-000519, g-000575, g-000516, g-000585, g-000486, g-000489, g-000539
g-000484, g-000502, g-000523, g-000595, g-000305, g-000574, g-000599, g-000589, g-000509, g-000538
g-000526, g-000551, g-000579, g-000590, g-000445, g-000556, g-000543, g-000501, g-000504, g-000570
PC_ 3
Positive: g-000015, g-000575, g-000483, g-000316, g-000025, g-000364, g-000050, g-000278, g-000443, g-000360
g-000332, g-000124, g-000212, g-000387, g-000536, g-000252, g-000251, g-000321, g-000501, g-000470
g-000582, g-000106, g-000455, g-000368, g-000081, g-000104, g-000437, g-000288, g-000386, g-000317
Negative: g-000211, g-000337, g-000129, g-000185, g-000397, g-000403, g-000253, g-000098, g-000390, g-000303
g-000052, g-000088, g-000463, g-000468, g-000236, g-000209, g-000005, g-000375, g-000342, g-000262
g-000388, g-000091, g-000413, g-000285, g-000003, g-000095, g-000142, g-000205, g-000432, g-000241
PC_ 4
Positive: g-000379, g-000193, g-000212, g-000434, g-000593, g-000513, g-000177, g-000223, g-000069, g-000131
g-000162, g-000345, g-000462, g-000484, g-000448, g-000229, g-000365, g-000302, g-000010, g-000366
g-000051, g-000535, g-000269, g-000270, g-000155, g-000529, g-000373, g-000008, g-000393, g-000306
Negative: g-000334, g-000398, g-000292, g-000095, g-000097, g-000202, g-000382, g-000195, g-000007, g-000079
g-000086, g-000240, g-000263, g-000317, g-000576, g-000557, g-000160, g-000154, g-000214, g-000228
g-000313, g-000053, g-000524, g-000374, g-000568, g-000188, g-000358, g-000528, g-000362, g-000150
PC_ 5
Positive: g-000451, g-000339, g-000295, g-000328, g-000544, g-000061, g-000227, g-000391, g-000556, g-000237
g-000067, g-000165, g-000449, g-000591, g-000087, g-000129, g-000197, g-000203, g-000487, g-000505
g-000333, g-000029, g-000271, g-000064, g-000583, g-000156, g-000448, g-000153, g-000526, g-000393
Negative: g-000518, g-000108, g-000186, g-000170, g-000401, g-000337, g-000047, g-000599, g-000432, g-000578
g-000042, g-000065, g-000493, g-000261, g-000533, g-000256, g-000560, g-000596, g-000368, g-000381
g-000535, g-000338, g-000215, g-000159, g-000365, g-000234, g-000173, g-000387, g-000225, g-000272
Computing nearest neighbor graph
Computing SNN
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
Number of nodes: 1200
Number of edges: 55489
Running Louvain algorithm with multilevel refinement...
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Maximum modularity in 10 random starts: 0.5973
Number of communities: 4
Elapsed time: 0 seconds
Used resolution for Seurat clusterization is: 0.8
02:14:05 UMAP embedding parameters a = 0.9922 b = 1.112
02:14:05 Read 1200 rows and found 50 numeric columns
02:14:06 Using Annoy for neighbor search, n_neighbors = 30
02:14:06 Building Annoy index with metric = cosine, n_trees = 50
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
02:14:06 Writing NN index file to temp file /tmp/Rtmpa9V7l9/filef72159fd697
02:14:06 Searching Annoy index using 1 thread, search_k = 3000
02:14:06 Annoy recall = 100%
02:14:07 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30
02:14:09 Initializing from normalized Laplacian + noise (using RSpectra)
02:14:09 Commencing optimization for 500 epochs, with 42270 positive edges
Using method 'umap'
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
02:14:13 Optimization finished
Creating PDF UMAP in file: /tmp/Rtmpa9V7l9/test/reclustering/pdf_umap_1.pdf
Creating Seurat object: DONE
* checking uniformity of cluster '0' of 4 clusters
Asked to drop 0 genes and 847 cells
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [353] cells
Estimate dispersion: START
Effective number of cores used: 1
Executing 1 genes batches from [1:600] to [1:600]
Estimate dispersion: DONE
dispersion | min: -0.038818359375 | max: 11.109375 | % negative: 5
Only analysis elapsed time: 3.34040307998657
Cotan genes' coex estimation started
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 avalable 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: 3.09359002113342
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.0132489204406738
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0521578788757324
Estimating genes' coex
Calculate genes' coex elapsed time: 0.97477912902832
Total calculations elapsed time: 4.13377594947815
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 5.12658500671387
Total elapsed time: 9.4263641834259
Checking uniformity for the cluster '01_0000' with 353 cells
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
S matrix sorted
Calculate GDI dataframe: DONE
GDI plot
Removed 0 low GDI genes (such as the fully-expressed) in GDI plot
Cluster 01_0000, with size 353, is uniform
0.83% of the genes is above the given GDI threshold 1.46
GDI 99% quantile is at 1.4439
cluster 01_0000 is uniform
* checking uniformity of cluster '1' of 4 clusters
Asked to drop 0 genes and 879 cells
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [321] cells
Estimate dispersion: START
Effective number of cores used: 1
Executing 1 genes batches from [1:600] to [1:600]
Estimate dispersion: DONE
dispersion | min: -0.0501708984375 | max: 14.515625 | % negative: 8.5
Only analysis elapsed time: 3.32627201080322
Cotan genes' coex estimation started
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 avalable 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: 3.07249307632446
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.0124080181121826
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0387988090515137
Estimating genes' coex
Calculate genes' coex elapsed time: 0.958570003509521
Total calculations elapsed time: 4.08226990699768
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 5.07749581336975
Total elapsed time: 9.36736297607422
Checking uniformity for the cluster '01_0001' with 321 cells
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
S matrix sorted
Calculate GDI dataframe: DONE
GDI plot
Removed 0 low GDI genes (such as the fully-expressed) in GDI plot
Cluster 01_0001, with size 321, is uniform
0.5% of the genes is above the given GDI threshold 1.46
GDI 99% quantile is at 1.4305
cluster 01_0001 is uniform
* checking uniformity of cluster '2' of 4 clusters
Asked to drop 0 genes and 905 cells
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [295] cells
Estimate dispersion: START
Effective number of cores used: 1
Executing 1 genes batches from [1:600] to [1:600]
Estimate dispersion: DONE
dispersion | min: -0.054443359375 | max: 104 | % negative: 36.5
Only analysis elapsed time: 3.3200581073761
Cotan genes' coex estimation started
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 avalable 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: 3.32006597518921
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.0143280029296875
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0254280567169189
Estimating genes' coex
Calculate genes' coex elapsed time: 1.09350299835205
Total calculations elapsed time: 4.45332503318787
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 5.51276588439941
Total elapsed time: 9.81489205360413
Checking uniformity for the cluster '01_0002' with 295 cells
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
S matrix sorted
Calculate GDI dataframe: DONE
GDI plot
Removed 0 low GDI genes (such as the fully-expressed) in GDI plot
Cluster 01_0002, with size 295, is uniform
0% of the genes is above the given GDI threshold 1.46
GDI 99% quantile is at 1.3925
cluster 01_0002 is uniform
* checking uniformity of cluster '3' of 4 clusters
Asked to drop 0 genes and 969 cells
Cotan analysis functions started
Asked to drop 1 genes and 0 cells
Genes/cells selection done: dropped [1] genes and [0] cells
Working on [599] genes and [231] cells
Estimate dispersion: START
Effective number of cores used: 1
Executing 1 genes batches from [1:599] to [1:599]
Estimate dispersion: DONE
dispersion | min: -0.0662841796875 | max: 82.5 | % negative: 33.889816360601
Only analysis elapsed time: 3.62985610961914
Cotan genes' coex estimation started
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 avalable 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: 3.44586491584778
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.0152451992034912
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0245299339294434
Estimating genes' coex
Calculate genes' coex elapsed time: 1.12764692306519
Total calculations elapsed time: 4.6132869720459
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 5.69618391990662
Total elapsed time: 10.4580428600311
Checking uniformity for the cluster '01_0003' with 231 cells
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
S matrix sorted
Calculate GDI dataframe: DONE
GDI plot
Removed 0 low GDI genes (such as the fully-expressed) in GDI plot
Cluster 01_0003, with size 231, is uniform
0% of the genes is above the given GDI threshold 1.46
GDI 99% quantile is at 1.373
cluster 01_0003 is uniform
Found 4 uniform and 0 non-uniform clusters
NO new possible uniform clusters! 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'
* DEA on cluster '2'
* DEA on cluster '3'
* DEA on cluster '4'
Differential Expression Analysis - DONE
Applied reordering to clusterization is:
1 -> 3, 2 -> 1, 3 -> 2, 4 -> 4
Cluster, UMAP and Saving the Seurat dataset
Computing nearest neighbor graph
Computing SNN
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
Number of nodes: 1200
Number of edges: 55489
Running Louvain algorithm with multilevel refinement...
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Maximum modularity in 10 random starts: 0.6846
Number of communities: 4
Elapsed time: 0 seconds
02:15:31 UMAP embedding parameters a = 0.9922 b = 1.112
02:15:31 Read 1200 rows and found 25 numeric columns
02:15:31 Using Annoy for neighbor search, n_neighbors = 30
02:15:31 Building Annoy index with metric = cosine, n_trees = 50
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
02:15:32 Writing NN index file to temp file /tmp/Rtmpa9V7l9/filef721f961177
02:15:32 Searching Annoy index using 1 thread, search_k = 3000
02:15:32 Annoy recall = 100%
02:15:33 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30
02:15:35 Initializing from normalized Laplacian + noise (using RSpectra)
02:15:35 Commencing optimization for 500 epochs, with 43428 positive edges
Using method 'umap'
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
02:15:40 Optimization finished
Creating cells' uniform clustering: DONE
Applied reordering to clusterization is:
1 -> 1, 2 -> 2, 3 -> 3, 4 -> 4
Asked to drop 0 genes and 905 cells
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [295] cells
Estimate dispersion: START
Effective number of cores used: 1
Executing 1 genes batches from [1:600] to [1:600]
Estimate dispersion: DONE
dispersion | min: -0.054443359375 | max: 104 | % negative: 36.5
Only analysis elapsed time: 3.46906518936157
Cotan genes' coex estimation started
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 avalable 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: 3.42636013031006
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.0169649124145508
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0241241455078125
Estimating genes' coex
Calculate genes' coex elapsed time: 1.04639196395874
Total calculations elapsed time: 4.51384115219116
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 5.61563301086426
Total elapsed time: 10.1117072105408
Checking uniformity for the cluster 'Cluster_2' with 295 cells
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
S matrix sorted
Calculate GDI dataframe: DONE
GDI plot
Removed 0 low GDI genes (such as the fully-expressed) in GDI plot
Cluster Cluster_2, with size 295, is uniform
0% of the genes is above the given GDI threshold 1.46
GDI 99% quantile is at 1.3925
Differential Expression Analysis - START
* DEA on cluster '-1'
* DEA on cluster '1'
* DEA on cluster '2'
* DEA on cluster '3'
* DEA on cluster '4'
Differential Expression Analysis - DONE
Applied reordering to clusterization is:
1 -> 2, 2 -> 1, 3 -> 4, 4 -> 3, -1 -> -1
Applied reordering to clusterization is:
1 -> 2, 2 -> 3, 3 -> 1, 4 -> 4, -1 -> -1
Creating cells' uniform clustering: START
In iteration 1 the number of cells to re-cluster is 1200 cells belonging to 0 clusters
Creating Seurat object: 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%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Centering and scaling data matrix
|
| | 0%
|
|======================================================================| 100%
PC_ 1
Positive: g-000558, g-000570, g-000499, g-000504, g-000546, g-000506, g-000503, g-000517, g-000596, g-000528
g-000527, g-000580, g-000592, g-000578, g-000509, g-000488, g-000555, g-000577, g-000534, g-000583
g-000598, g-000535, g-000512, g-000554, g-000519, g-000525, g-000548, g-000544, g-000502, g-000541
Negative: g-000133, g-000007, g-000074, g-000141, g-000057, g-000235, g-000170, g-000019, g-000195, g-000140
g-000183, g-000031, g-000046, g-000178, g-000177, g-000161, g-000157, g-000139, g-000011, g-000135
g-000125, g-000208, g-000061, g-000085, g-000204, g-000104, g-000237, g-000004, g-000038, g-000128
PC_ 2
Positive: g-000039, g-000050, g-000175, g-000078, g-000116, g-000189, g-000135, g-000047, g-000072, g-000087
g-000063, g-000235, g-000066, g-000109, g-000018, g-000074, g-000231, g-000136, g-000034, g-000207
g-000128, g-000167, g-000171, g-000049, g-000182, g-000013, g-000054, g-000062, g-000240, g-000158
Negative: g-000584, g-000583, g-000544, g-000519, g-000575, g-000516, g-000585, g-000486, g-000489, g-000539
g-000484, g-000502, g-000523, g-000595, g-000305, g-000574, g-000599, g-000589, g-000509, g-000538
g-000526, g-000551, g-000579, g-000590, g-000445, g-000556, g-000543, g-000501, g-000504, g-000570
PC_ 3
Positive: g-000015, g-000575, g-000483, g-000316, g-000025, g-000364, g-000050, g-000278, g-000443, g-000360
g-000332, g-000124, g-000212, g-000387, g-000536, g-000252, g-000251, g-000321, g-000501, g-000470
g-000582, g-000106, g-000455, g-000368, g-000081, g-000104, g-000437, g-000288, g-000386, g-000317
Negative: g-000211, g-000337, g-000129, g-000185, g-000397, g-000403, g-000253, g-000098, g-000390, g-000303
g-000052, g-000088, g-000463, g-000468, g-000236, g-000209, g-000005, g-000375, g-000342, g-000262
g-000388, g-000091, g-000413, g-000285, g-000003, g-000095, g-000142, g-000205, g-000432, g-000241
PC_ 4
Positive: g-000379, g-000193, g-000212, g-000434, g-000593, g-000513, g-000177, g-000223, g-000069, g-000131
g-000162, g-000345, g-000462, g-000484, g-000448, g-000229, g-000365, g-000302, g-000010, g-000366
g-000051, g-000535, g-000269, g-000270, g-000155, g-000529, g-000373, g-000008, g-000393, g-000306
Negative: g-000334, g-000398, g-000292, g-000095, g-000097, g-000202, g-000382, g-000195, g-000007, g-000079
g-000086, g-000240, g-000263, g-000317, g-000576, g-000557, g-000160, g-000154, g-000214, g-000228
g-000313, g-000053, g-000524, g-000374, g-000568, g-000188, g-000358, g-000528, g-000362, g-000150
PC_ 5
Positive: g-000451, g-000339, g-000295, g-000328, g-000544, g-000061, g-000227, g-000391, g-000556, g-000237
g-000067, g-000165, g-000449, g-000591, g-000087, g-000129, g-000197, g-000203, g-000487, g-000505
g-000333, g-000029, g-000271, g-000064, g-000583, g-000156, g-000448, g-000153, g-000526, g-000393
Negative: g-000518, g-000108, g-000186, g-000170, g-000401, g-000337, g-000047, g-000599, g-000432, g-000578
g-000042, g-000065, g-000493, g-000261, g-000533, g-000256, g-000560, g-000596, g-000368, g-000381
g-000535, g-000338, g-000215, g-000159, g-000365, g-000234, g-000173, g-000387, g-000225, g-000272
Computing nearest neighbor graph
Computing SNN
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
Number of nodes: 1200
Number of edges: 55489
Running Louvain algorithm with multilevel refinement...
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Maximum modularity in 10 random starts: 0.5973
Number of communities: 4
Elapsed time: 0 seconds
Used resolution for Seurat clusterization is: 0.8
02:16:05 UMAP embedding parameters a = 0.9922 b = 1.112
02:16:05 Read 1200 rows and found 50 numeric columns
02:16:05 Using Annoy for neighbor search, n_neighbors = 30
02:16:05 Building Annoy index with metric = cosine, n_trees = 50
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
02:16:06 Writing NN index file to temp file /tmp/Rtmpa9V7l9/filef72176b5e883
02:16:06 Searching Annoy index using 1 thread, search_k = 3000
02:16:06 Annoy recall = 100%
02:16:07 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30
02:16:09 Initializing from normalized Laplacian + noise (using RSpectra)
02:16:09 Commencing optimization for 500 epochs, with 42270 positive edges
Using method 'umap'
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
02:16:14 Optimization finished
Creating PDF UMAP in file: /tmp/Rtmpa9V7l9/test/reclustering/pdf_umap_1.pdf
Creating Seurat object: DONE
Using passed in clusterization
* checking uniformity of cluster '1' of 2 clusters
Asked to drop 0 genes and 600 cells
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [600] cells
Estimate dispersion: START
Effective number of cores used: 1
Executing 1 genes batches from [1:600] to [1:600]
Estimate dispersion: DONE
dispersion | min: -0.0386962890625 | max: 19.40625 | % negative: 6.5
Only analysis elapsed time: 4.05959701538086
Cotan genes' coex estimation started
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: 3.54814004898071
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.0145759582519531
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0624930858612061
Estimating genes' coex
Calculate genes' coex elapsed time: 1.05661511421204
Total calculations elapsed time: 4.68182420730591
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 5.71596097946167
Total elapsed time: 10.8511700630188
Checking uniformity for the cluster '01_0001' with 600 cells
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
S matrix sorted
Calculate GDI dataframe: DONE
GDI plot
Removed 0 low GDI genes (such as the fully-expressed) in GDI plot
Cluster 01_0001, with size 600, is uniform
1% of the genes is above the given GDI threshold 1.46
GDI 99% quantile is at 1.4534
cluster 01_0001 is uniform
* checking uniformity of cluster '2' of 2 clusters
Asked to drop 0 genes and 600 cells
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [600] cells
Estimate dispersion: START
Effective number of cores used: 1
Executing 1 genes batches from [1:600] to [1:600]
Estimate dispersion: DONE
dispersion | min: -0.032958984375 | max: 10.0859375 | % negative: 3.66666666666667
Only analysis elapsed time: 3.65967488288879
Cotan genes' coex estimation started
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: 3.47800207138062
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.0127098560333252
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.064608097076416
Estimating genes' coex
Calculate genes' coex elapsed time: 1.0098078250885
Total calculations elapsed time: 4.56512784957886
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 5.58917093276978
Total elapsed time: 10.2480669021606
Checking uniformity for the cluster '01_0002' with 600 cells
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
S matrix sorted
Calculate GDI dataframe: DONE
GDI plot
Removed 0 low GDI genes (such as the fully-expressed) in GDI plot
Cluster 01_0002, with size 600, is uniform
0.5% of the genes is above the given GDI threshold 1.46
GDI 99% quantile is at 1.4378
cluster 01_0002 is uniform
Found 2 uniform and 0 non-uniform clusters
NO new possible uniform clusters! Unclustered cell left: 0
The final raw clusterization contains [ 2 ] different clusters: 01_0001, 01_0002
Differential Expression Analysis - START
* DEA on cluster '1'
* DEA on cluster '2'
Differential Expression Analysis - DONE
Applied reordering to clusterization is:
1 -> 1, 2 -> 2
Cluster, UMAP and Saving the Seurat dataset
Computing nearest neighbor graph
Computing SNN
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
Number of nodes: 1200
Number of edges: 55489
Running Louvain algorithm with multilevel refinement...
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Maximum modularity in 10 random starts: 0.6846
Number of communities: 4
Elapsed time: 0 seconds
02:16:56 UMAP embedding parameters a = 0.9922 b = 1.112
02:16:57 Read 1200 rows and found 25 numeric columns
02:16:57 Using Annoy for neighbor search, n_neighbors = 30
02:16:57 Building Annoy index with metric = cosine, n_trees = 50
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
02:16:57 Writing NN index file to temp file /tmp/Rtmpa9V7l9/filef7217e48a8ad
02:16:57 Searching Annoy index using 1 thread, search_k = 3000
02:16:57 Annoy recall = 100%
02:16:58 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30
02:17:00 Initializing from normalized Laplacian + noise (using RSpectra)
02:17:00 Commencing optimization for 500 epochs, with 43428 positive edges
Using method 'umap'
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
02:17:04 Optimization finished
Creating cells' uniform clustering: DONE
findClustersMarkers - START
clustersDeltaExpression - START
Handling cluster '1' with mean UDE 1.20998115359079
Handling cluster '2' with mean UDE 0.538244816501366
Handling cluster '3' with mean UDE 1.43530796540674
Handling cluster '4' with mean UDE 0.632684489354434
clustersDeltaExpression - DONE
Log Fold Change Analysis - START
* Analysis of cluster: '1'
* Analysis of cluster: '2'
* Analysis of cluster: '3'
* Analysis of cluster: '4'
Log Fold Change Analysis - DONE
findClustersMarkers - DONE
findClustersMarkers - START
clustersDeltaExpression - START
Handling cluster '1' with mean UDE 1.20998115359079
Handling cluster '2' with mean UDE 0.538244816501366
Handling cluster '3' with mean UDE 1.43530796540674
Handling cluster '4' with mean UDE 0.632684489354434
clustersDeltaExpression - DONE
Log Fold Change Analysis - START
* Analysis of cluster: '1'
* Analysis of cluster: '2'
* Analysis of cluster: '3'
* Analysis of cluster: '4'
Log Fold Change Analysis - DONE
findClustersMarkers - DONE
findClustersMarkers - START
Differential Expression Analysis - START
* DEA on cluster '1'
* DEA on cluster '2'
* DEA on cluster '3'
* DEA on cluster '4'
Differential Expression Analysis - DONE
clustersDeltaExpression - START
Handling cluster '1' with mean UDE 1.20998115359079
Handling cluster '2' with mean UDE 0.538244816501366
Handling cluster '3' with mean UDE 1.43530796540674
Handling cluster '4' with mean UDE 0.632684489354434
clustersDeltaExpression - DONE
Log Fold Change Analysis - START
* Analysis of cluster: '1'
* Analysis of cluster: '2'
* Analysis of cluster: '3'
* Analysis of cluster: '4'
Log Fold Change Analysis - DONE
findClustersMarkers - DONE
[1] "1"
Asked to drop 0 genes and 879 cells
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [321] cells
Estimate dispersion: START
Effective number of cores used: 1
Executing 1 genes batches from [1:600] to [1:600]
Estimate dispersion: DONE
dispersion | min: -0.0501708984375 | max: 14.515625 | % negative: 8.5
Only analysis elapsed time: 3.80063605308533
Cotan genes' coex estimation started
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 avalable 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: 3.67956113815308
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.0147459506988525
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0446169376373291
Estimating genes' coex
Calculate genes' coex elapsed time: 1.09703803062439
Total calculations elapsed time: 4.83596205711365
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 5.9158239364624
Total elapsed time: 10.8557329177856
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
S matrix sorted
Calculate GDI dataframe: DONE
[1] "3"
Asked to drop 0 genes and 847 cells
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [353] cells
Estimate dispersion: START
Effective number of cores used: 1
Executing 1 genes batches from [1:600] to [1:600]
Estimate dispersion: DONE
dispersion | min: -0.038818359375 | max: 11.109375 | % negative: 5
Only analysis elapsed time: 3.67476916313171
Cotan genes' coex estimation started
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 avalable 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: 3.53882193565369
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.0134961605072021
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0639488697052002
Estimating genes' coex
Calculate genes' coex elapsed time: 1.07424807548523
Total calculations elapsed time: 4.69051504135132
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 5.78112101554871
Total elapsed time: 10.570522069931
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
S matrix sorted
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 [1200] cells
Estimate dispersion: START
Effective number of cores used: 1
Executing 1 genes batches from [1:600] to [1:600]
Estimate dispersion: DONE
dispersion | min: 0.2197265625 | max: 6.08056640625 | % negative: 0
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [1200] cells
Estimate dispersion: START
Effective number of cores used: 1
Executing 1 genes batches from [1:600] to [1:600]
Estimate dispersion: DONE
dispersion | min: 0.2197265625 | max: 6.08056640625 | % negative: 0
Only analysis elapsed time: 4.69438600540161
Cotan genes' coex estimation started
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: 4.09185385704041
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.0136151313781738
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0764350891113281
Estimating genes' coex
Calculate genes' coex elapsed time: 1.09103679656982
Total calculations elapsed time: 5.27294087409973
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 6.36089396476746
Total elapsed time: 12.1222457885742
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
calculating PValues: DONE
Number of selected secondary markers: 109
Calculating S: START
Calculating S: DONE
S matrix sorted
Number of columns (V set - secondary markers): 109
Number of rows (U set): 60
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
calculating PValues: DONE
Number of selected secondary markers: 109
Calculating S: START
Calculating S: DONE
S matrix sorted
Number of columns (V set - secondary markers): 109
Number of rows (U set): 60
Calculating gene co-expression space - DONE
Establishing gene clusters - DONE
Initializing `COTAN` meta-data
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [1200] cells
Estimate dispersion: START
Effective number of cores used: 1
Executing 1 genes batches from [1:600] to [1:600]
Estimate dispersion: DONE
dispersion | min: 0.2197265625 | max: 6.08056640625 | % negative: 0
Cotan genes' coex estimation not requested
Total elapsed time: 6.820631980896
Differential Expression Analysis - START
* DEA on cluster '1'
* DEA on cluster '2'
* DEA on cluster '3'
* DEA on cluster '4'
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'
Log Fold Change Analysis - DONE
clustersDeltaExpression - START
Handling cluster '1' with mean UDE 1.43530796540674
Handling cluster '2' with mean UDE 0.640931107489519
Handling cluster '3' with mean UDE 0.546546914955575
Handling cluster '4' with mean UDE 1.22034802329657
clustersDeltaExpression - DONE
In group G1 there are 3 detected over 3 genes
In group G2 there are 2 detected over 2 genes
In group G3 there are 5 detected over 5 genes
Merging cells' uniform clustering: START
Start merging nearest clusters: iteration 1
Differential Expression Analysis - START
* DEA on cluster '1'
* DEA on cluster '2'
* DEA on cluster '3'
* DEA on cluster '4'
Differential Expression Analysis - DONE
Clusters pairs for merging:
c("1", "2") c("3", "4") c("2", "3") c("2", "4") c("1", "3") c("1", "4")
*1_2-merge
Asked to drop 0 genes and 626 cells
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [574] cells
Estimate dispersion: START
Effective number of cores used: 1
Executing 1 genes batches from [1:600] to [1:600]
Estimate dispersion: DONE
dispersion | min: -0.0340576171875 | max: 10.4375 | % negative: 4.33333333333333
Only analysis elapsed time: 3.71468091011047
Cotan genes' coex estimation started
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 avalable 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: 3.71397399902344
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.0178089141845703
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0562620162963867
Estimating genes' coex
Calculate genes' coex elapsed time: 1.10920596122742
Total calculations elapsed time: 4.89725089073181
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 5.98112392425537
Total elapsed time: 10.7646129131317
Checking uniformity for the cluster '1_2-merge' with 574 cells
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
S matrix sorted
Calculate GDI dataframe: DONE
GDI plot
Removed 0 low GDI genes (such as the fully-expressed) in GDI plot
Cluster 1_2-merge, with size 574, is uniform
0.67% of the genes is above the given GDI threshold 1.46
GDI 99% quantile is at 1.4297
Clusters 1 and 2 can be merged
*3_4-merge
Asked to drop 0 genes and 574 cells
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [626] cells
Estimate dispersion: START
Effective number of cores used: 1
Executing 1 genes batches from [1:600] to [1:600]
Estimate dispersion: DONE
dispersion | min: -0.03839111328125 | max: 17.40625 | % negative: 6.66666666666667
Only analysis elapsed time: 3.7337110042572
Cotan genes' coex estimation started
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 avalable 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: 3.44222807884216
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.0124859809875488
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0523219108581543
Estimating genes' coex
Calculate genes' coex elapsed time: 1.03638195991516
Total calculations elapsed time: 4.54341793060303
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 5.56399893760681
Total elapsed time: 10.3540101051331
Checking uniformity for the cluster '3_4-merge' with 626 cells
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
S matrix sorted
Calculate GDI dataframe: DONE
GDI plot
Removed 0 low GDI genes (such as the fully-expressed) in GDI plot
Cluster 3_4-merge, with size 626, is uniform
1% of the genes is above the given GDI threshold 1.46
GDI 99% quantile is at 1.4544
Clusters 3 and 4 can be merged
*Clusters 2 or 3 is now missing due to previous merges: skip.
*Clusters 2 or 4 is now missing due to previous merges: skip.
*Clusters 1 or 3 is now missing due to previous merges: skip.
*Clusters 1 or 4 is now missing due to previous merges: skip.
Executed 2 merges out of 6
Start merging nearest clusters: iteration 2
Differential Expression Analysis - START
* DEA on cluster '1_2-merge'
* DEA on cluster '3_4-merge'
Differential Expression Analysis - DONE
Clusters pairs for merging:
c("1_2-merge", "3_4-merge")
*1_2-merge_3_4-merge-merge
Asked to drop no genes or cells
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [1200] cells
Estimate dispersion: START
Effective number of cores used: 1
Executing 1 genes batches from [1:600] to [1:600]
Estimate dispersion: DONE
dispersion | min: 0.2197265625 | max: 6.08056640625 | % negative: 0
Only analysis elapsed time: 4.43817090988159
Cotan genes' coex estimation started
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 avalable 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: 3.8052659034729
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.0152640342712402
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0766010284423828
Estimating genes' coex
Calculate genes' coex elapsed time: 1.04709696769714
Total calculations elapsed time: 4.94422793388367
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 5.97550296783447
Total elapsed time: 11.4725029468536
Checking uniformity for the cluster '1_2-merge_3_4-merge-merge' with 1200 cells
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
S matrix sorted
Calculate GDI dataframe: 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 1200, is not uniform
22.17% of the genes is above the given GDI threshold 1.46
GDI 99% quantile is at 1.6405
Merging clusters 1_2-merge and 3_4-merge results in a too high GDI
None of the 1 nearest cluster pairs could be merged
The final merged clusterization contains [2] different clusters: 1_2-merge, 3_4-merge
Differential Expression Analysis - START
* DEA on cluster '1'
* DEA on cluster '2'
Differential Expression Analysis - DONE
Applied reordering to clusterization is:
1 -> 1, 2 -> 2
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'
Log Fold Change Analysis - DONE
Asked to drop 0 genes and 626 cells
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [574] cells
Estimate dispersion: START
Effective number of cores used: 1
Executing 1 genes batches from [1:600] to [1:600]
Estimate dispersion: DONE
dispersion | min: -0.0340576171875 | max: 10.4375 | % negative: 4.33333333333333
Only analysis elapsed time: 3.67419600486755
Cotan genes' coex estimation started
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 avalable 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: 3.3672251701355
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.0131878852844238
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0545029640197754
Estimating genes' coex
Calculate genes' coex elapsed time: 0.989538192749023
Total calculations elapsed time: 4.42445421218872
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 5.36961984634399
Total elapsed time: 10.0915398597717
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
S matrix sorted
Calculate GDI dataframe: DONE
Asked to drop 0 genes and 574 cells
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [626] cells
Estimate dispersion: START
Effective number of cores used: 1
Executing 1 genes batches from [1:600] to [1:600]
Estimate dispersion: DONE
dispersion | min: -0.03839111328125 | max: 17.40625 | % negative: 6.66666666666667
Only analysis elapsed time: 3.53886985778809
Cotan genes' coex estimation started
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 avalable 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: 3.19354796409607
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.0122809410095215
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.05218505859375
Estimating genes' coex
Calculate genes' coex elapsed time: 0.992999076843262
Total calculations elapsed time: 4.2510130405426
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 5.13884210586548
Total elapsed time: 9.70464706420898
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
S matrix sorted
Calculate GDI dataframe: DONE
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 433 ]
>
> proc.time()
user system elapsed
665.290 8.038 766.254
COTAN.Rcheck/COTAN-Ex.timings
| name | user | system | elapsed | |
| COTAN-Legacy | 0.005 | 0.001 | 0.007 | |
| COTANObjectCreation | 11.201 | 0.377 | 12.959 | |
| CalculatingCOEX | 61.521 | 1.159 | 72.144 | |
| ClustersList | 0.015 | 0.005 | 0.021 | |
| GenesStatistics | 11.689 | 0.219 | 14.129 | |
| HandleMetaData | 0.143 | 0.020 | 0.189 | |
| HandlingClusterizations | 35.538 | 0.831 | 43.548 | |
| HandlingConditions | 0.189 | 0.008 | 0.230 | |
| HeatmapPlots | 61.153 | 2.003 | 74.007 | |
| LoggingFunctions | 0.006 | 0.003 | 0.012 | |
| ParametersEstimations | 32.748 | 0.808 | 39.013 | |
| RawDataCleaning | 10.727 | 0.349 | 12.675 | |
| RawDataGetters | 0.137 | 0.008 | 0.172 | |
| UniformClusters | 166.538 | 1.709 | 191.778 | |
| getColorsVector | 0.002 | 0.001 | 0.005 | |