From cc871a9a052b249546c3a33f2d7dac615f30c51a Mon Sep 17 00:00:00 2001 From: Zeyuan-Chen Date: Thu, 11 Jan 2024 06:43:12 +0000 Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20cozygene?= =?UTF-8?q?/Unico@2d2a6b4df4ae2d33652f03b6cb3c2538e27d944f=20=F0=9F=9A=80?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- articles/Unico-Tutorial.html | 7 +++++++ pkgdown.yml | 2 +- reference/Unico.html | 16 ++++++++-------- reference/association_asymptotic.html | 24 ++++++++++++------------ reference/association_parametric.html | 24 ++++++++++++------------ reference/simulate_data.html | 4 ++-- reference/tensor.html | 24 ++++++++++++------------ 7 files changed, 54 insertions(+), 47 deletions(-) diff --git a/articles/Unico-Tutorial.html b/articles/Unico-Tutorial.html index 4a40a02..7451311 100644 --- a/articles/Unico-Tutorial.html +++ b/articles/Unico-Tutorial.html @@ -88,10 +88,17 @@

Unico-Tutorial

+
+

Load the Unico package and +

 library(Unico)
 library(matrixStats)
+
+#For visualization in this vignette
+install.packages(c("ggplot2","ggpubr","hexbin"))
 source("https://github.com/cozygene/Unico/raw/main/vignettes/vignetts.utils.r")
+

Deconvolution on pseudobulk RNA expression data

diff --git a/pkgdown.yml b/pkgdown.yml index a8afab4..822ab9f 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -3,5 +3,5 @@ pkgdown: 2.0.7 pkgdown_sha: ~ articles: Unico-Tutorial: Unico-Tutorial.html -last_built: 2024-01-11T05:47Z +last_built: 2024-01-11T06:42Z diff --git a/reference/Unico.html b/reference/Unico.html index dff41fc..7738ee0 100644 --- a/reference/Unico.html +++ b/reference/Unico.html @@ -232,17 +232,17 @@

Details

Examples

data = simulate_data(n = 100, m = 2, k = 3, p1 = 1, p2 = 1, taus_std = 0, log_file = NULL)
-#> INFO [2024-01-11 05:47:23] Start simulation ...
-#> INFO [2024-01-11 05:47:23] Finished simulation
+#> INFO [2024-01-11 06:43:02] Start simulation ...
+#> INFO [2024-01-11 06:43:02] Finished simulation
 res = list()
 res$params.hat = Unico(data$X, data$W, data$C1, data$C2, parallel=FALSE, log_file=NULL)
-#> INFO [2024-01-11 05:47:23] Starting Unico ...
-#> INFO [2024-01-11 05:47:23] Validate Unico inputs
-#> INFO [2024-01-11 05:47:23] Starting parameter learning ...
+#> INFO [2024-01-11 06:43:02] Starting Unico ...
+#> INFO [2024-01-11 06:43:02] Validate Unico inputs
+#> INFO [2024-01-11 06:43:02] Starting parameter learning ...
 #> 
  |                                                  | 0 % ~calculating  
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  
-#> INFO [2024-01-11 05:47:23] Formating results ...
-#> INFO [2024-01-11 05:47:23] Capping extreme values in estimated parameters
-#> INFO [2024-01-11 05:47:23] Finished parameter learning
+#> INFO [2024-01-11 06:43:02] Formating results ...
+#> INFO [2024-01-11 06:43:02] Capping extreme values in estimated parameters
+#> INFO [2024-01-11 06:43:02] Finished parameter learning
diff --git a/reference/association_asymptotic.html b/reference/association_asymptotic.html index 3f98451..a891734 100644 --- a/reference/association_asymptotic.html +++ b/reference/association_asymptotic.html @@ -183,24 +183,24 @@

Details

Examples

data = simulate_data(n = 100, m = 2, k = 3, p1 = 1, p2 = 1, taus_std = 0, log_file = NULL)
-#> INFO [2024-01-11 05:47:23] Start simulation ...
-#> INFO [2024-01-11 05:47:23] Finished simulation
+#> INFO [2024-01-11 06:43:03] Start simulation ...
+#> INFO [2024-01-11 06:43:03] Finished simulation
 res = list()
 res$params.hat = Unico(data$X, data$W, data$C1, data$C2, parallel=FALSE, log_file=NULL)
-#> INFO [2024-01-11 05:47:23] Starting Unico ...
-#> INFO [2024-01-11 05:47:23] Validate Unico inputs
-#> INFO [2024-01-11 05:47:23] Starting parameter learning ...
+#> INFO [2024-01-11 06:43:03] Starting Unico ...
+#> INFO [2024-01-11 06:43:03] Validate Unico inputs
+#> INFO [2024-01-11 06:43:03] Starting parameter learning ...
 #> 
  |                                                  | 0 % ~calculating  
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  
-#> INFO [2024-01-11 05:47:24] Formating results ...
-#> INFO [2024-01-11 05:47:24] Capping extreme values in estimated parameters
-#> INFO [2024-01-11 05:47:24] Finished parameter learning
+#> INFO [2024-01-11 06:43:03] Formating results ...
+#> INFO [2024-01-11 06:43:03] Capping extreme values in estimated parameters
+#> INFO [2024-01-11 06:43:03] Finished parameter learning
 res$params.hat = association_asymptotic(data$X, res$params.hat, parallel=FALSE, log_file=NULL)
-#> INFO [2024-01-11 05:47:24] Validate asymptotic inputs ...
+#> INFO [2024-01-11 06:43:03] Validate asymptotic inputs ...
 #> [1] 2 1
-#> INFO [2024-01-11 05:47:24] Preparing weights for asymptotic pvals calculation ...
-#> INFO [2024-01-11 05:47:24] Starting asymptotic pvals calculation: asymptotic ...
+#> INFO [2024-01-11 06:43:03] Preparing weights for asymptotic pvals calculation ...
+#> INFO [2024-01-11 06:43:03] Starting asymptotic pvals calculation: asymptotic ...
 #> 
  |                                                  | 0 % ~calculating  
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  
-#> INFO [2024-01-11 05:47:24] Finished asymptotic pvals calculation: asymptotic
+#> INFO [2024-01-11 06:43:03] Finished asymptotic pvals calculation: asymptotic
diff --git a/reference/association_parametric.html b/reference/association_parametric.html index c4fa678..1c6786e 100644 --- a/reference/association_parametric.html +++ b/reference/association_parametric.html @@ -182,23 +182,23 @@

Details

Examples

data = simulate_data(n = 100, m = 2, k = 3, p1 = 1, p2 = 1, taus_std = 0, log_file = NULL)
-#> INFO [2024-01-11 05:47:24] Start simulation ...
-#> INFO [2024-01-11 05:47:24] Finished simulation
+#> INFO [2024-01-11 06:43:03] Start simulation ...
+#> INFO [2024-01-11 06:43:03] Finished simulation
 res = list()
 res$params.hat = Unico(data$X, data$W, data$C1, data$C2, parallel=FALSE, log_file=NULL)
-#> INFO [2024-01-11 05:47:24] Starting Unico ...
-#> INFO [2024-01-11 05:47:24] Validate Unico inputs
-#> INFO [2024-01-11 05:47:24] Starting parameter learning ...
+#> INFO [2024-01-11 06:43:03] Starting Unico ...
+#> INFO [2024-01-11 06:43:03] Validate Unico inputs
+#> INFO [2024-01-11 06:43:03] Starting parameter learning ...
 #> 
  |                                                  | 0 % ~calculating  
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  
-#> INFO [2024-01-11 05:47:24] Formating results ...
-#> INFO [2024-01-11 05:47:24] Capping extreme values in estimated parameters
-#> INFO [2024-01-11 05:47:24] Finished parameter learning
+#> INFO [2024-01-11 06:43:04] Formating results ...
+#> INFO [2024-01-11 06:43:04] Capping extreme values in estimated parameters
+#> INFO [2024-01-11 06:43:04] Finished parameter learning
 res$params.hat = association_parametric(data$X, res$params.hat, parallel=FALSE, log_file=NULL)
-#> INFO [2024-01-11 05:47:24] Validate parametric inputs ...
-#> INFO [2024-01-11 05:47:24] Preparing weights for parametric pvals calculation ...
-#> INFO [2024-01-11 05:47:24] Starting parametric pvals calculation: parametric ...
+#> INFO [2024-01-11 06:43:04] Validate parametric inputs ...
+#> INFO [2024-01-11 06:43:04] Preparing weights for parametric pvals calculation ...
+#> INFO [2024-01-11 06:43:04] Starting parametric pvals calculation: parametric ...
 #> 
  |                                                  | 0 % ~calculating  
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  
-#> INFO [2024-01-11 05:47:24] Finished parametric pvals calculation: parametric
+#> INFO [2024-01-11 06:43:04] Finished parametric pvals calculation: parametric
diff --git a/reference/simulate_data.html b/reference/simulate_data.html index f1b61d3..0585bb2 100644 --- a/reference/simulate_data.html +++ b/reference/simulate_data.html @@ -193,8 +193,8 @@

Details

Examples

sim.data = simulate_data(n = 100, m = 5, k = 5, p1 = 1, p2 = 2, log_file = NULL)
-#> INFO [2024-01-11 05:47:24] Start simulation ...
-#> INFO [2024-01-11 05:47:24] Finished simulation
+#> INFO [2024-01-11 06:43:04] Start simulation ...
+#> INFO [2024-01-11 06:43:04] Finished simulation
diff --git a/reference/tensor.html b/reference/tensor.html index dab3dd9..f044756 100644 --- a/reference/tensor.html +++ b/reference/tensor.html @@ -133,23 +133,23 @@

Details

Examples

data = simulate_data(n = 100, m = 2, k = 3, p1 = 1, p2 = 1, taus_std = 0, log_file = NULL)
-#> INFO [2024-01-11 05:47:25] Start simulation ...
-#> INFO [2024-01-11 05:47:25] Finished simulation
+#> INFO [2024-01-11 06:43:04] Start simulation ...
+#> INFO [2024-01-11 06:43:04] Finished simulation
 res = list()
 res$params.hat = Unico(data$X, data$W, data$C1, data$C2, parallel=FALSE, log_file=NULL)
-#> INFO [2024-01-11 05:47:25] Starting Unico ...
-#> INFO [2024-01-11 05:47:25] Validate Unico inputs
-#> INFO [2024-01-11 05:47:25] Starting parameter learning ...
+#> INFO [2024-01-11 06:43:04] Starting Unico ...
+#> INFO [2024-01-11 06:43:04] Validate Unico inputs
+#> INFO [2024-01-11 06:43:04] Starting parameter learning ...
 #> 
  |                                                  | 0 % ~calculating  
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  
-#> INFO [2024-01-11 05:47:25] Formating results ...
-#> INFO [2024-01-11 05:47:25] Capping extreme values in estimated parameters
-#> INFO [2024-01-11 05:47:25] Finished parameter learning
+#> INFO [2024-01-11 06:43:04] Formating results ...
+#> INFO [2024-01-11 06:43:04] Capping extreme values in estimated parameters
+#> INFO [2024-01-11 06:43:04] Finished parameter learning
 res$Z = tensor(data$X, data$W, data$C1, data$C2, res$params.hat, parallel=FALSE, log_file=NULL)
-#> INFO [2024-01-11 05:47:25] Validate tensor inputs ...
-#> INFO [2024-01-11 05:47:25] Starting tensor ...
+#> INFO [2024-01-11 06:43:04] Validate tensor inputs ...
+#> INFO [2024-01-11 06:43:04] Starting tensor ...
 #> 
  |                                                  | 0 % ~calculating  
  |+++++++++++++++++++++++++                         | 50% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  
-#> INFO [2024-01-11 05:47:25] Formating tensor result ...
-#> INFO [2024-01-11 05:47:25] Finished tensor estimation
+#> INFO [2024-01-11 06:43:04] Formating tensor result ...
+#> INFO [2024-01-11 06:43:04] Finished tensor estimation