From d4c6bf453ecfc85cc04599794a42b002123b31e7 Mon Sep 17 00:00:00 2001 From: lcolladotor Date: Fri, 5 Apr 2024 20:09:57 +0000 Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20LieberIn?= =?UTF-8?q?stitute/spatialLIBD@db1e73351f0fec26ee81997e4d0777581046fb8b=20?= =?UTF-8?q?=F0=9F=9A=80?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- articles/TenX_data_download.html | 18 ++++++------ articles/guide_to_spatial_registration.html | 30 ++++++++++---------- articles/multi_gene_plots.html | 8 +++--- articles/spatialLIBD.html | 12 ++++---- index.html | 2 +- pkgdown.yml | 2 +- reference/add_images.html | 26 ++++++++--------- reference/add_key.html | 2 +- reference/annotate_registered_clusters.html | 2 +- reference/check_modeling_results.html | 2 +- reference/check_sce.html | 2 +- reference/check_sce_layer.html | 2 +- reference/check_spe.html | 2 +- reference/cluster_export.html | 2 +- reference/cluster_import.html | 6 ++-- reference/fetch_data.html | 2 +- reference/frame_limits.html | 2 +- reference/gene_set_enrichment.html | 2 +- reference/gene_set_enrichment_plot.html | 2 +- reference/geom_spatial.html | 2 +- reference/get_colors.html | 2 +- reference/img_edit.html | 2 +- reference/img_update.html | 2 +- reference/img_update_all.html | 2 +- reference/layer_boxplot.html | 4 +-- reference/layer_stat_cor.html | 2 +- reference/layer_stat_cor_plot.html | 2 +- reference/registration_block_cor.html | 12 ++++---- reference/registration_model.html | 8 +++--- reference/registration_pseudobulk.html | 6 ++-- reference/registration_stats_anova.html | 18 ++++++------ reference/registration_stats_enrichment.html | 20 ++++++------- reference/registration_stats_pairwise.html | 20 ++++++------- reference/registration_wrapper.html | 24 ++++++++-------- reference/sce_to_spe.html | 2 +- reference/sig_genes_extract.html | 4 +-- reference/sig_genes_extract_all.html | 4 +-- reference/vis_clus.html | 2 +- reference/vis_clus_p.html | 2 +- reference/vis_gene.html | 2 +- reference/vis_gene_p.html | 2 +- reference/vis_grid_clus.html | 2 +- reference/vis_grid_gene.html | 2 +- 43 files changed, 137 insertions(+), 137 deletions(-) diff --git a/articles/TenX_data_download.html b/articles/TenX_data_download.html index 2553d940..2307b290 100644 --- a/articles/TenX_data_download.html +++ b/articles/TenX_data_download.html @@ -535,7 +535,7 @@

From Gencode## Show the GTF cache location gtf_cache #> BFC4 -#> "/github/home/.cache/R/BiocFileCache/11591564e576_gencode.v32.annotation.gtf.gz" +#> "/github/home/.cache/R/BiocFileCache/115b3c00be56_gencode.v32.annotation.gtf.gz" ## Import into R (takes ~1 min) gtf <- rtracklayer::import(gtf_cache) @@ -821,11 +821,11 @@

Wrapper functions= c("lowres", "hires", "detected", "aligned"), load = TRUE, reference_gtf = gtf_cache ) -#> 2024-04-05 20:04:46.379983 SpatialExperiment::read10xVisium: reading basic data from SpaceRanger -#> 2024-04-05 20:04:57.746735 read10xVisiumAnalysis: reading analysis output from SpaceRanger -#> 2024-04-05 20:04:58.777167 add10xVisiumAnalysis: adding analysis output from SpaceRanger -#> 2024-04-05 20:04:59.029908 rtracklayer::import: reading the reference GTF file -#> 2024-04-05 20:05:25.977095 adding gene information to the SPE object +#> 2024-04-05 20:06:46.12981 SpatialExperiment::read10xVisium: reading basic data from SpaceRanger +#> 2024-04-05 20:06:57.507888 read10xVisiumAnalysis: reading analysis output from SpaceRanger +#> 2024-04-05 20:06:58.544382 add10xVisiumAnalysis: adding analysis output from SpaceRanger +#> 2024-04-05 20:06:58.794619 rtracklayer::import: reading the reference GTF file +#> 2024-04-05 20:07:25.395402 adding gene information to the SPE object #> Warning: Gene IDs did not match. This typically happens when you are not using #> the same GTF file as the one that was used by SpaceRanger. For example, one #> file uses GENCODE IDs and the other one ENSEMBL IDs. read10xVisiumWrapper() @@ -833,7 +833,7 @@

Wrapper functions#> Warning: Dropping 29 out of 36601 genes for which we don't have information on #> the reference GTF file. This typically happens when you are not using the same #> GTF file as the one that was used by SpaceRanger. -#> 2024-04-05 20:05:27.439796 adding information used by spatialLIBD +#> 2024-04-05 20:07:26.874497 adding information used by spatialLIBD 
 ## Run our shiny app
 if (interactive()) {
@@ -1117,9 +1117,9 @@ 
Reproducibilitylibrary("knitr")
 knit("TenX_data_download.Rmd", tangle = TRUE)

Date the vignette was generated.

-
#> [1] "2024-04-05 20:05:28 UTC"
+
#> [1] "2024-04-05 20:07:28 UTC"

Wallclock time spent generating the vignette.

-
#> Time difference of 1.781 mins
+
#> Time difference of 1.79 mins

R session information.

#> ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
 #>  setting  value
diff --git a/articles/guide_to_spatial_registration.html b/articles/guide_to_spatial_registration.html
index f76bb9ca..1e1e8550 100644
--- a/articles/guide_to_spatial_registration.html
+++ b/articles/guide_to_spatial_registration.html
@@ -287,7 +287,7 @@ 
Spatial Reference
 ## get reference layer enrichment statistics
 layer_modeling_results <- fetch_data(type = "modeling_results")
-#> 2024-04-05 20:05:47.05775 loading file /github/home/.cache/R/BiocFileCache/11592b032277_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
+#> 2024-04-05 20:07:48.06424 loading file /github/home/.cache/R/BiocFileCache/115b6b55de6b_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
 
 layer_modeling_results$enrichment[1:5, 1:5]
 #>    t_stat_WM t_stat_Layer1 t_stat_Layer2 t_stat_Layer3 t_stat_Layer4
@@ -389,18 +389,18 @@ 
Get Enrichment statistics
     gene_ensembl = "gene_id",
     gene_name = "gene_name"
 )
-#> 2024-04-05 20:05:54.605212 make pseudobulk object
-#> 2024-04-05 20:05:56.27116 dropping 13 pseudo-bulked samples that are below 'min_ncells'.
-#> 2024-04-05 20:05:56.330158 drop lowly expressed genes
-#> 2024-04-05 20:05:56.50757 normalize expression
-#> 2024-04-05 20:05:57.954918 create model matrix
-#> 2024-04-05 20:05:57.979144 run duplicateCorrelation()
-#> 2024-04-05 20:06:11.317145 The estimated correlation is: 0.138734774807097
-#> 2024-04-05 20:06:11.319783 computing enrichment statistics
-#> 2024-04-05 20:06:12.414152 extract and reformat enrichment results
-#> 2024-04-05 20:06:12.466076 running the baseline pairwise model
-#> 2024-04-05 20:06:12.622605 computing pairwise statistics
-#> 2024-04-05 20:06:13.930996 computing F-statistics

+#> 2024-04-05 20:07:55.729548 make pseudobulk object
+#> 2024-04-05 20:07:57.406807 dropping 13 pseudo-bulked samples that are below 'min_ncells'.
+#> 2024-04-05 20:07:57.468537 drop lowly expressed genes
+#> 2024-04-05 20:07:57.669501 normalize expression
+#> 2024-04-05 20:07:59.128324 create model matrix
+#> 2024-04-05 20:07:59.152507 run duplicateCorrelation()
+#> 2024-04-05 20:08:12.466311 The estimated correlation is: 0.138734774807097
+#> 2024-04-05 20:08:12.46879 computing enrichment statistics
+#> 2024-04-05 20:08:13.52675 extract and reformat enrichment results
+#> 2024-04-05 20:08:13.578985 running the baseline pairwise model
+#> 2024-04-05 20:08:13.754707 computing pairwise statistics
+#> 2024-04-05 20:08:15.065329 computing F-statistics

Extract Enrichment t-statistics @@ -560,9 +560,9 @@

Reproducibilitylibrary("knitr") knit("guide_to_spatial_registration.Rmd", tangle = TRUE)

Date the vignette was generated.

-
#> [1] "2024-04-05 20:06:15 UTC"
+
#> [1] "2024-04-05 20:08:16 UTC"

Wallclock time spent generating the vignette.

-
#> Time difference of 40.931 secs
+
#> Time difference of 42.017 secs

R session information.

#> ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
 #>  setting  value
diff --git a/articles/multi_gene_plots.html b/articles/multi_gene_plots.html
index 74d2934a..4a0b5b92 100644
--- a/articles/multi_gene_plots.html
+++ b/articles/multi_gene_plots.html
@@ -197,9 +197,9 @@ 
Plotting One Gene
 modeling_results <- fetch_data(type = "modeling_results")
-#> 2024-04-05 20:06:38.485929 loading file /github/home/.cache/R/BiocFileCache/11592b032277_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
+#> 2024-04-05 20:08:40.97899 loading file /github/home/.cache/R/BiocFileCache/115b6b55de6b_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
 sce_layer <- fetch_data(type = "sce_layer")
-#> 2024-04-05 20:06:39.406176 loading file /github/home/.cache/R/BiocFileCache/11597ad98e84_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-04-05 20:08:42.230782 loading file /github/home/.cache/R/BiocFileCache/115b403d7ac1_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
 sig_genes <- sig_genes_extract_all(
     n = 400,
     modeling_results = modeling_results,
@@ -423,9 +423,9 @@ 
Reproducibilitylibrary("knitr")
 knit("multi_gene_plots.Rmd", tangle = TRUE)

 
Date the vignette was generated.

-
#> [1] "2024-04-05 20:06:55 UTC"

+
#> [1] "2024-04-05 20:08:58 UTC"

 
Wallclock time spent generating the vignette.

-
#> Time difference of 36.951 secs

+
#> Time difference of 38.808 secs

 
R session information.

 
#> ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
 #>  setting  value
diff --git a/articles/spatialLIBD.html b/articles/spatialLIBD.html
index cb683ee7..70b0b24e 100644
--- a/articles/spatialLIBD.html
+++ b/articles/spatialLIBD.html
@@ -417,7 +417,7 @@ 
Downloading the data with s
 
 ## Download the small example sce data
 sce <- fetch_data(type = "sce_example", eh = ehub)
-#> 2024-04-05 20:07:11.47321 loading file /github/home/.cache/R/BiocFileCache/11593b8b56cb_sce_sub_for_vignette.Rdata%3Fdl%3D1
+#> 2024-04-05 20:09:15.429788 loading file /github/home/.cache/R/BiocFileCache/115b36d9e52_sce_sub_for_vignette.Rdata%3Fdl%3D1
 
 ## Convert to a SpatialExperiment object
 spe <- sce_to_spe(sce)
@@ -429,9 +429,9 @@ 
Downloading the data with s
 
 ## Query ExperimentHub and download the data
 if (!exists("sce_layer")) sce_layer <- fetch_data(type = "sce_layer", eh = ehub)
-#> 2024-04-05 20:07:15.965327 loading file /github/home/.cache/R/BiocFileCache/11597ad98e84_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-04-05 20:09:21.29669 loading file /github/home/.cache/R/BiocFileCache/115b403d7ac1_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
 modeling_results <- fetch_data("modeling_results", eh = ehub)
-#> 2024-04-05 20:07:16.409124 loading file /github/home/.cache/R/BiocFileCache/11592b032277_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1

+#> 2024-04-05 20:09:21.747998 loading file /github/home/.cache/R/BiocFileCache/115b6b55de6b_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1

 
Once you have downloaded the objects, we can explore them a little
 bit

 
@@ -504,7 +504,7 @@ 
Downloading the data with s
         )
 )
 #>    user  system elapsed 
-#>   9.855   0.432  10.306
+#>   9.888   0.484  10.381
 
 ## Explore the result
 class(sig_genes)
@@ -1380,9 +1380,9 @@ 
Reproducibilitylibrary("knitr")
 knit("spatialLIBD.Rmd", tangle = TRUE)

 
Date the vignette was generated.

-
#> [1] "2024-04-05 20:07:34 UTC"

+
#> [1] "2024-04-05 20:09:39 UTC"

 
Wallclock time spent generating the vignette.

-
#> Time difference of 35.419 secs

+
#> Time difference of 37.369 secs

 
R session information.

 
#> ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
 #>  setting  value
diff --git a/index.html b/index.html
index 26dedc9b..04a80f0d 100644
--- a/index.html
+++ b/index.html
@@ -539,7 +539,7 @@ 
Dev status

 
  • Bioc last commit
    • 
 
  • Bioc dependencies
    • 
 
  • Codecov test coverage
    • 
-
  • R build status
    • 
+
  • R build status
    • 
 
  • GitHub issues
    • 
 
  • GitHub pulls
    • 
 
  • DOI
    • 
diff --git a/pkgdown.yml b/pkgdown.yml
index cee0dc65..865d58f0 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -6,5 +6,5 @@ articles:
   guide_to_spatial_registration: guide_to_spatial_registration.html
   multi_gene_plots: multi_gene_plots.html
   spatialLIBD: spatialLIBD.html
-last_built: 2024-04-05T19:58Z
+last_built: 2024-04-05T19:59Z
 
diff --git a/reference/add_images.html b/reference/add_images.html
index 3f3acdb1..a1825593 100644
--- a/reference/add_images.html
+++ b/reference/add_images.html
@@ -165,29 +165,29 @@ 
    Examples
    
         image_paths = c("151507" = "https://spatial-dlpfc.s3.us-east-2.amazonaws.com/images/151507_tissue_lowres_image.png")
     ))
 }
-#> 2024-04-05 19:58:24.996743 loading file /github/home/.cache/R/BiocFileCache/155f98a302_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
-#> 2024-04-05 19:58:40.609337 adding image for sample 151507
-#> 2024-04-05 19:58:41.338532 adding image for sample 151508
+#> 2024-04-05 20:00:03.124019 loading file /github/home/.cache/R/BiocFileCache/1560561f15f7_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-04-05 20:00:19.145376 adding image for sample 151507
+#> 2024-04-05 20:00:20.898775 adding image for sample 151508
 #> Warning: No image was found for sample: 151508
-#> 2024-04-05 19:58:41.338855 adding image for sample 151509
+#> 2024-04-05 20:00:20.899117 adding image for sample 151509
 #> Warning: No image was found for sample: 151509
-#> 2024-04-05 19:58:41.339072 adding image for sample 151510
+#> 2024-04-05 20:00:20.899331 adding image for sample 151510
 #> Warning: No image was found for sample: 151510
-#> 2024-04-05 19:58:41.339273 adding image for sample 151669
+#> 2024-04-05 20:00:20.899534 adding image for sample 151669
 #> Warning: No image was found for sample: 151669
-#> 2024-04-05 19:58:41.339472 adding image for sample 151670
+#> 2024-04-05 20:00:20.899734 adding image for sample 151670
 #> Warning: No image was found for sample: 151670
-#> 2024-04-05 19:58:41.339661 adding image for sample 151671
+#> 2024-04-05 20:00:20.899927 adding image for sample 151671
 #> Warning: No image was found for sample: 151671
-#> 2024-04-05 19:58:41.339851 adding image for sample 151672
+#> 2024-04-05 20:00:20.900118 adding image for sample 151672
 #> Warning: No image was found for sample: 151672
-#> 2024-04-05 19:58:41.340041 adding image for sample 151673
+#> 2024-04-05 20:00:20.900309 adding image for sample 151673
 #> Warning: No image was found for sample: 151673
-#> 2024-04-05 19:58:41.340232 adding image for sample 151674
+#> 2024-04-05 20:00:20.900553 adding image for sample 151674
 #> Warning: No image was found for sample: 151674
-#> 2024-04-05 19:58:41.340424 adding image for sample 151675
+#> 2024-04-05 20:00:20.900764 adding image for sample 151675
 #> Warning: No image was found for sample: 151675
-#> 2024-04-05 19:58:41.340619 adding image for sample 151676
+#> 2024-04-05 20:00:20.900966 adding image for sample 151676
 #> Warning: No image was found for sample: 151676
 #> DataFrame with 13 rows and 4 columns
 #>       sample_id    image_id   data scaleFactor
diff --git a/reference/add_key.html b/reference/add_key.html
index 52f8800e..d072b0d1 100644
--- a/reference/add_key.html
+++ b/reference/add_key.html
@@ -117,7 +117,7 @@ 
    Examples
    
     ## Note that the original 'key' order was 'sample_id'_'barcode' and we'
     ## have since changed it to 'barcode'_'sample_id'.
 }
-#> 2024-04-05 19:58:43.40326 loading file /github/home/.cache/R/BiocFileCache/155f98a302_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-04-05 20:00:23.587719 loading file /github/home/.cache/R/BiocFileCache/1560561f15f7_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
 #> [1] "AAACAACGAATAGTTC-1_151507" "AAACAAGTATCTCCCA-1_151507"
 #> [3] "AAACAATCTACTAGCA-1_151507" "AAACACCAATAACTGC-1_151507"
 #> [5] "AAACAGCTTTCAGAAG-1_151507" "AAACAGGGTCTATATT-1_151507"
diff --git a/reference/annotate_registered_clusters.html b/reference/annotate_registered_clusters.html
index 04d383e3..675dba5c 100644
--- a/reference/annotate_registered_clusters.html
+++ b/reference/annotate_registered_clusters.html
@@ -139,7 +139,7 @@ 
    Examples
    
 if (!exists("modeling_results")) {
     modeling_results <- fetch_data(type = "modeling_results")
 }
-#> 2024-04-05 19:58:57.92285 loading file /github/home/.cache/R/BiocFileCache/11592b032277_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
+#> 2024-04-05 20:00:38.680408 loading file /github/home/.cache/R/BiocFileCache/115b6b55de6b_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
 
 ## Compute the correlations
 cor_stats_layer <- layer_stat_cor(
diff --git a/reference/check_modeling_results.html b/reference/check_modeling_results.html
index ceb0500b..e34e931c 100644
--- a/reference/check_modeling_results.html
+++ b/reference/check_modeling_results.html
@@ -108,7 +108,7 @@ 
    Examples
    
 if (!exists("modeling_results")) {
     modeling_results <- fetch_data(type = "modeling_results")
 }
-#> 2024-04-05 19:58:58.831466 loading file /github/home/.cache/R/BiocFileCache/11592b032277_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
+#> 2024-04-05 20:00:40.02132 loading file /github/home/.cache/R/BiocFileCache/115b6b55de6b_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
 
 ## Check the object
 xx <- check_modeling_results(modeling_results)
diff --git a/reference/check_sce.html b/reference/check_sce.html
index b52ee553..cdb461eb 100644
--- a/reference/check_sce.html
+++ b/reference/check_sce.html
@@ -131,7 +131,7 @@ 
    Examples
    
     ## Check the object
     check_sce(sce_example)
 }
-#> 2024-04-05 19:58:59.752855 loading file /github/home/.cache/R/BiocFileCache/11593b8b56cb_sce_sub_for_vignette.Rdata%3Fdl%3D1
+#> 2024-04-05 20:00:41.402931 loading file /github/home/.cache/R/BiocFileCache/115b36d9e52_sce_sub_for_vignette.Rdata%3Fdl%3D1
 #> class: SingleCellExperiment 
 #> dim: 33538 47681 
 #> metadata(1): image
diff --git a/reference/check_sce_layer.html b/reference/check_sce_layer.html
index f4976477..fbd35244 100644
--- a/reference/check_sce_layer.html
+++ b/reference/check_sce_layer.html
@@ -111,7 +111,7 @@ 
    Examples
    
     
    
 ## Obtain the necessary data
 if (!exists("sce_layer")) sce_layer <- fetch_data("sce_layer")
-#> 2024-04-05 19:59:02.128027 loading file /github/home/.cache/R/BiocFileCache/11597ad98e84_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-04-05 20:00:44.308081 loading file /github/home/.cache/R/BiocFileCache/115b403d7ac1_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
 
 ## Check the object
 check_sce_layer(sce_layer)
diff --git a/reference/check_spe.html b/reference/check_spe.html
index 2ca1a131..bfe7894d 100644
--- a/reference/check_spe.html
+++ b/reference/check_spe.html
@@ -123,7 +123,7 @@ 
    Examples
    
     ## Check the object
     check_spe(spe)
 }
-#> 2024-04-05 19:59:03.978877 loading file /github/home/.cache/R/BiocFileCache/155f98a302_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-04-05 20:00:46.59603 loading file /github/home/.cache/R/BiocFileCache/1560561f15f7_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
 #> class: SpatialExperiment 
 #> dim: 33538 47681 
 #> metadata(0):
diff --git a/reference/cluster_export.html b/reference/cluster_export.html
index 5a272448..3ad3954b 100644
--- a/reference/cluster_export.html
+++ b/reference/cluster_export.html
@@ -134,7 +134,7 @@ 
    Examples
    
     cluster_export(spe, "spatialLIBD")
     cluster_export(spe, "GraphBased")
 }
-#> 2024-04-05 19:59:18.470286 loading file /github/home/.cache/R/BiocFileCache/155f98a302_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-04-05 20:01:01.877567 loading file /github/home/.cache/R/BiocFileCache/1560561f15f7_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
 #> Overwriting 'spe$key'. Set 'overwrite = FALSE' if you do not want to overwrite it.
 #> Overwriting 'spe$key'. Set 'overwrite = FALSE' if you do not want to overwrite it.
 
    
diff --git a/reference/cluster_import.html b/reference/cluster_import.html
index 09c988d2..c87c23e3 100644
--- a/reference/cluster_import.html
+++ b/reference/cluster_import.html
@@ -137,11 +137,11 @@ 
    Examples
    
     ## Re-import them
     colData(cluster_import(spe))
 }
-#> 2024-04-05 19:59:32.667595 loading file /github/home/.cache/R/BiocFileCache/155f98a302_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-04-05 20:01:16.840454 loading file /github/home/.cache/R/BiocFileCache/1560561f15f7_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
 #> Overwriting 'spe$key'. Set 'overwrite = FALSE' if you do not want to overwrite it.
-#> Warning: '/tmp/RtmpgLjxXM/exported_clusters/spatialLIBD' already exists
+#> Warning: '/tmp/Rtmpl5MUOg/exported_clusters/spatialLIBD' already exists
 #> Overwriting 'spe$key'. Set 'overwrite = FALSE' if you do not want to overwrite it.
-#> Warning: '/tmp/RtmpgLjxXM/exported_clusters/GraphBased' already exists
+#> Warning: '/tmp/Rtmpl5MUOg/exported_clusters/GraphBased' already exists
 #> Overwriting 'spe$key'. Set 'overwrite = FALSE' if you do not want to overwrite it.
 #> DataFrame with 47681 rows and 71 columns
 #>                                       key   sample_id   Cluster   sum_umi
diff --git a/reference/fetch_data.html b/reference/fetch_data.html
index a2a133b7..02a2f14a 100644
--- a/reference/fetch_data.html
+++ b/reference/fetch_data.html
@@ -165,7 +165,7 @@ 
    Examples
    
 ## Download the SingleCellExperiment object
 ## at the layer-level
 if (!exists("sce_layer")) sce_layer <- fetch_data("sce_layer")
-#> 2024-04-05 19:59:47.859114 loading file /github/home/.cache/R/BiocFileCache/11597ad98e84_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-04-05 20:01:33.003093 loading file /github/home/.cache/R/BiocFileCache/115b403d7ac1_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
 
 ## Explore the data
 sce_layer
diff --git a/reference/frame_limits.html b/reference/frame_limits.html
index 216bbc70..283b75a6 100644
--- a/reference/frame_limits.html
+++ b/reference/frame_limits.html
@@ -154,7 +154,7 @@ 
    Examples
    
     ## Obtain the frame limits for one sample
     frame_limits(spe, sampleid = "151673")
 }
-#> 2024-04-05 19:59:49.476695 loading file /github/home/.cache/R/BiocFileCache/155f98a302_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-04-05 20:01:35.173933 loading file /github/home/.cache/R/BiocFileCache/1560561f15f7_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
 #> $y_min
 #> [1] 64
 #> 
diff --git a/reference/gene_set_enrichment.html b/reference/gene_set_enrichment.html
index 5bc094c7..afbfa05c 100644
--- a/reference/gene_set_enrichment.html
+++ b/reference/gene_set_enrichment.html
@@ -176,7 +176,7 @@ 
    Examples
    
 if (!exists("modeling_results")) {
     modeling_results <- fetch_data(type = "modeling_results")
 }
-#> 2024-04-05 20:00:04.267055 loading file /github/home/.cache/R/BiocFileCache/11592b032277_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
+#> 2024-04-05 20:01:50.66524 loading file /github/home/.cache/R/BiocFileCache/115b6b55de6b_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
 
 ## Compute the gene set enrichment results
 asd_sfari_enrichment <- gene_set_enrichment(
diff --git a/reference/gene_set_enrichment_plot.html b/reference/gene_set_enrichment_plot.html
index a2a1503e..a165053d 100644
--- a/reference/gene_set_enrichment_plot.html
+++ b/reference/gene_set_enrichment_plot.html
@@ -178,7 +178,7 @@ 
    Examples
    
 if (!exists("modeling_results")) {
     modeling_results <- fetch_data(type = "modeling_results")
 }
-#> 2024-04-05 20:00:05.476083 loading file /github/home/.cache/R/BiocFileCache/11592b032277_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
+#> 2024-04-05 20:01:52.315443 loading file /github/home/.cache/R/BiocFileCache/115b6b55de6b_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
 
 ## Compute the gene set enrichment results
 asd_sfari_enrichment <- gene_set_enrichment(
diff --git a/reference/geom_spatial.html b/reference/geom_spatial.html
index 5665d87a..ee9c0d4b 100644
--- a/reference/geom_spatial.html
+++ b/reference/geom_spatial.html
@@ -175,7 +175,7 @@ 
    Examples
    
     ## Clean up
     rm(spe_sub)
 }
-#> 2024-04-05 20:00:07.238809 loading file /github/home/.cache/R/BiocFileCache/155f98a302_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-04-05 20:01:54.538708 loading file /github/home/.cache/R/BiocFileCache/1560561f15f7_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
 
 
    
     
diff --git a/reference/get_colors.html b/reference/get_colors.html
index 823b5d7d..d1437cd4 100644
--- a/reference/get_colors.html
+++ b/reference/get_colors.html
@@ -105,7 +105,7 @@ 
    Examples
    
     
    
 ## Obtain the necessary data
 if (!exists("sce_layer")) sce_layer <- fetch_data("sce_layer")
-#> 2024-04-05 20:00:22.551161 loading file /github/home/.cache/R/BiocFileCache/11597ad98e84_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-04-05 20:02:10.842966 loading file /github/home/.cache/R/BiocFileCache/115b403d7ac1_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
 
 ## Example layer colors with the corresponding names
 get_colors(libd_layer_colors, sce_layer$layer_guess)
diff --git a/reference/img_edit.html b/reference/img_edit.html
index 18742337..cc29ddff 100644
--- a/reference/img_edit.html
+++ b/reference/img_edit.html
@@ -222,7 +222,7 @@ 
    Examples
    
     x <- img_edit(spe, sampleid = "151507", brightness = 25)
     plot(x)
 }
-#> 2024-04-05 20:00:23.635238 loading file /github/home/.cache/R/BiocFileCache/155f98a302_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-04-05 20:02:12.361915 loading file /github/home/.cache/R/BiocFileCache/1560561f15f7_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
 
 
    
     
diff --git a/reference/img_update.html b/reference/img_update.html
index f01a72ed..b02ce585 100644
--- a/reference/img_update.html
+++ b/reference/img_update.html
@@ -139,7 +139,7 @@ 
    Examples
    
     ## Reduce brightness to 25% and update the imgData()
     imgData(img_update(spe, sampleid = "151507", brightness = 25))
 }
-#> 2024-04-05 20:00:39.204887 loading file /github/home/.cache/R/BiocFileCache/155f98a302_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-04-05 20:02:28.610867 loading file /github/home/.cache/R/BiocFileCache/1560561f15f7_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
 #> DataFrame with 13 rows and 4 columns
 #>       sample_id      image_id   data scaleFactor
 #>     <character>   <character> <list>   <numeric>
diff --git a/reference/img_update_all.html b/reference/img_update_all.html
index e84bb674..b9e2c6f9 100644
--- a/reference/img_update_all.html
+++ b/reference/img_update_all.html
@@ -138,7 +138,7 @@ 
    Examples
    
     ## update the imgData()
     imgData(img_update_all(spe, brightness = 25))
 }
-#> 2024-04-05 20:00:53.415044 loading file /github/home/.cache/R/BiocFileCache/155f98a302_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-04-05 20:02:43.333119 loading file /github/home/.cache/R/BiocFileCache/1560561f15f7_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
 #> DataFrame with 24 rows and 4 columns
 #>       sample_id      image_id   data scaleFactor
 #>     <character>   <character> <list>   <numeric>
diff --git a/reference/layer_boxplot.html b/reference/layer_boxplot.html
index 2678b8e3..cbc40a03 100644
--- a/reference/layer_boxplot.html
+++ b/reference/layer_boxplot.html
@@ -185,9 +185,9 @@ 
    Examples
    
 if (!exists("modeling_results")) {
     modeling_results <- fetch_data(type = "modeling_results")
 }
-#> 2024-04-05 20:01:10.230575 loading file /github/home/.cache/R/BiocFileCache/11592b032277_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
+#> 2024-04-05 20:03:00.531552 loading file /github/home/.cache/R/BiocFileCache/115b6b55de6b_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
 if (!exists("sce_layer")) sce_layer <- fetch_data(type = "sce_layer")
-#> 2024-04-05 20:01:11.073344 loading file /github/home/.cache/R/BiocFileCache/11597ad98e84_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-04-05 20:03:01.79801 loading file /github/home/.cache/R/BiocFileCache/115b403d7ac1_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
 
 ## Top 2 genes from the enrichment model
 sig_genes <- sig_genes_extract_all(
diff --git a/reference/layer_stat_cor.html b/reference/layer_stat_cor.html
index 708fc7d0..93eeacac 100644
--- a/reference/layer_stat_cor.html
+++ b/reference/layer_stat_cor.html
@@ -156,7 +156,7 @@ 
    Examples
    
 if (!exists("modeling_results")) {
     modeling_results <- fetch_data(type = "modeling_results")
 }
-#> 2024-04-05 20:01:14.179337 loading file /github/home/.cache/R/BiocFileCache/11592b032277_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
+#> 2024-04-05 20:03:05.811506 loading file /github/home/.cache/R/BiocFileCache/115b6b55de6b_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
 
 ## Compute the correlations
 cor_stats_layer <- layer_stat_cor(
diff --git a/reference/layer_stat_cor_plot.html b/reference/layer_stat_cor_plot.html
index 010966e5..6a50ede7 100644
--- a/reference/layer_stat_cor_plot.html
+++ b/reference/layer_stat_cor_plot.html
@@ -145,7 +145,7 @@ 
    Examples
    
 if (!exists("modeling_results")) {
     modeling_results <- fetch_data(type = "modeling_results")
 }
-#> 2024-04-05 20:01:15.199864 loading file /github/home/.cache/R/BiocFileCache/11592b032277_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
+#> 2024-04-05 20:03:07.277842 loading file /github/home/.cache/R/BiocFileCache/115b6b55de6b_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
 
 ## Compute the correlations
 cor_stats_layer <- layer_stat_cor(
diff --git a/reference/registration_block_cor.html b/reference/registration_block_cor.html
index 98d1c584..63aa1503 100644
--- a/reference/registration_block_cor.html
+++ b/reference/registration_block_cor.html
@@ -146,9 +146,9 @@ 
    Examples
    
 #> 
 #> rgstr_> ## Pseudo-bulk
 #> rgstr_> sce_pseudo <- registration_pseudobulk(sce, "Cell_Cycle", "sample_id", c("age"), min_ncells = NULL)
-#> 2024-04-05 20:01:17.209751 make pseudobulk object
-#> 2024-04-05 20:01:18.270705 drop lowly expressed genes
-#> 2024-04-05 20:01:18.342654 normalize expression
+#> 2024-04-05 20:03:09.307972 make pseudobulk object
+#> 2024-04-05 20:03:10.369723 drop lowly expressed genes
+#> 2024-04-05 20:03:10.443448 normalize expression
 #> 
 #> rgstr_> colData(sce_pseudo)
 #> DataFrame with 20 rows and 8 columns
@@ -180,7 +180,7 @@ 
    Examples
    
 #> E_S                      S                      E        11
 #> 
 #> rgstr_> registration_mod <- registration_model(sce_pseudo, "age")
-#> 2024-04-05 20:01:18.422912 create model matrix
+#> 2024-04-05 20:03:10.525761 create model matrix
 #> 
 #> rgstr_> head(registration_mod)
 #>      registration_variableG0 registration_variableG1 registration_variableG2M
@@ -198,8 +198,8 @@ 
    Examples
    
 #> E_G0                      0 20.97006
 #> A_G1                      0 19.18719
 block_cor <- registration_block_cor(sce_pseudo, registration_mod)
-#> 2024-04-05 20:01:18.435945 run duplicateCorrelation()
-#> 2024-04-05 20:01:19.750538 The estimated correlation is: -0.0187869166526901
+#> 2024-04-05 20:03:10.540396 run duplicateCorrelation()
+#> 2024-04-05 20:03:11.833898 The estimated correlation is: -0.0187869166526901
    diff --git a/reference/registration_model.html b/reference/registration_model.html index d3587404..5cdb99ef 100644 --- a/reference/registration_model.html +++ b/reference/registration_model.html @@ -148,9 +148,9 @@

    Examples

    #> #> rgstr_> ## Pseudo-bulk #> rgstr_> sce_pseudo <- registration_pseudobulk(sce, "Cell_Cycle", "sample_id", c("age"), min_ncells = NULL) -#> 2024-04-05 20:01:20.153205 make pseudobulk object -#> 2024-04-05 20:01:20.37593 drop lowly expressed genes -#> 2024-04-05 20:01:20.431063 normalize expression +#> 2024-04-05 20:03:12.232176 make pseudobulk object +#> 2024-04-05 20:03:12.455766 drop lowly expressed genes +#> 2024-04-05 20:03:12.511126 normalize expression #> #> rgstr_> colData(sce_pseudo) #> DataFrame with 20 rows and 8 columns @@ -181,7 +181,7 @@

    Examples

    #> D_S S D 14 #> E_S S E 11 registration_mod <- registration_model(sce_pseudo, "age") -#> 2024-04-05 20:01:20.5066 create model matrix +#> 2024-04-05 20:03:12.585741 create model matrix head(registration_mod) #> registration_variableG0 registration_variableG1 registration_variableG2M #> A_G0 1 0 0 diff --git a/reference/registration_pseudobulk.html b/reference/registration_pseudobulk.html index 677b0e44..cd3196e7 100644 --- a/reference/registration_pseudobulk.html +++ b/reference/registration_pseudobulk.html @@ -159,9 +159,9 @@

    Examples

    ## Pseudo-bulk sce_pseudo <- registration_pseudobulk(sce, "Cell_Cycle", "sample_id", c("age"), min_ncells = NULL) -#> 2024-04-05 20:01:20.920686 make pseudobulk object -#> 2024-04-05 20:01:21.077883 drop lowly expressed genes -#> 2024-04-05 20:01:21.132482 normalize expression +#> 2024-04-05 20:03:13.001161 make pseudobulk object +#> 2024-04-05 20:03:13.163723 drop lowly expressed genes +#> 2024-04-05 20:03:13.218609 normalize expression colData(sce_pseudo) #> DataFrame with 20 rows and 8 columns #> Mutation_Status Cell_Cycle Treatment sample_id age diff --git a/reference/registration_stats_anova.html b/reference/registration_stats_anova.html index b3b56ff6..289d0eea 100644 --- a/reference/registration_stats_anova.html +++ b/reference/registration_stats_anova.html @@ -180,9 +180,9 @@

    Examples

    #> #> rgstr_> ## Pseudo-bulk #> rgstr_> sce_pseudo <- registration_pseudobulk(sce, "Cell_Cycle", "sample_id", c("age"), min_ncells = NULL) -#> 2024-04-05 20:01:21.740629 make pseudobulk object -#> 2024-04-05 20:01:21.89548 drop lowly expressed genes -#> 2024-04-05 20:01:21.949466 normalize expression +#> 2024-04-05 20:03:13.843174 make pseudobulk object +#> 2024-04-05 20:03:14.002436 drop lowly expressed genes +#> 2024-04-05 20:03:14.058592 normalize expression #> #> rgstr_> colData(sce_pseudo) #> DataFrame with 20 rows and 8 columns @@ -214,7 +214,7 @@

    Examples

    #> E_S S E 11 #> #> rgstr_> registration_mod <- registration_model(sce_pseudo, "age") -#> 2024-04-05 20:01:22.023612 create model matrix +#> 2024-04-05 20:03:14.135525 create model matrix #> #> rgstr_> head(registration_mod) #> registration_variableG0 registration_variableG1 registration_variableG2M @@ -233,13 +233,13 @@

    Examples

    #> A_G1 0 19.18719 #> #> rgst__> block_cor <- registration_block_cor(sce_pseudo, registration_mod) -#> 2024-04-05 20:01:22.03481 run duplicateCorrelation() -#> 2024-04-05 20:01:23.343878 The estimated correlation is: -0.0187869166526901 +#> 2024-04-05 20:03:14.146872 run duplicateCorrelation() +#> 2024-04-05 20:03:15.446322 The estimated correlation is: -0.0187869166526901 results_anova <- registration_stats_anova(sce_pseudo, block_cor, "age", gene_ensembl = "ensembl", gene_name = "gene_name", suffix = "example" ) -#> 2024-04-05 20:01:23.356266 computing F-statistics +#> 2024-04-05 20:03:15.46058 computing F-statistics head(results_anova) #> f_stat_example p_value_example fdr_example AveExpr_example ensembl gene #> 1 0.1328075 0.93918553 0.9951876 5.499488 ENSG1 gene1 @@ -254,7 +254,7 @@

    Examples

    block_cor = NaN, "age", gene_ensembl = "ensembl", gene_name = "gene_name", suffix = "example" ) -#> 2024-04-05 20:01:23.419196 computing F-statistics +#> 2024-04-05 20:03:15.532212 computing F-statistics head(results_anova_nan) #> f_stat_example p_value_example fdr_example AveExpr_example ensembl gene #> 1 0.1357180 0.93736053 0.9943765 5.499488 ENSG1 gene1 @@ -276,7 +276,7 @@

    Examples

    covars = NULL, gene_ensembl = "ensembl", gene_name = "gene_name", suffix = "nocovar" ) -#> 2024-04-05 20:01:23.469443 computing F-statistics +#> 2024-04-05 20:03:15.583129 computing F-statistics head(results_anova_nocovar) #> f_stat_nocovar p_value_nocovar fdr_nocovar AveExpr_nocovar ensembl gene #> 1 0.1393641 0.9351345 0.9962097 5.499488 ENSG1 gene1 diff --git a/reference/registration_stats_enrichment.html b/reference/registration_stats_enrichment.html index 5b741714..14c2b6d7 100644 --- a/reference/registration_stats_enrichment.html +++ b/reference/registration_stats_enrichment.html @@ -171,9 +171,9 @@

    Examples

    #> #> rgstr_> ## Pseudo-bulk #> rgstr_> sce_pseudo <- registration_pseudobulk(sce, "Cell_Cycle", "sample_id", c("age"), min_ncells = NULL) -#> 2024-04-05 20:01:24.023903 make pseudobulk object -#> 2024-04-05 20:01:24.180267 drop lowly expressed genes -#> 2024-04-05 20:01:24.234851 normalize expression +#> 2024-04-05 20:03:16.191147 make pseudobulk object +#> 2024-04-05 20:03:16.352778 drop lowly expressed genes +#> 2024-04-05 20:03:16.407234 normalize expression #> #> rgstr_> colData(sce_pseudo) #> DataFrame with 20 rows and 8 columns @@ -205,7 +205,7 @@

    Examples

    #> E_S S E 11 #> #> rgstr_> registration_mod <- registration_model(sce_pseudo, "age") -#> 2024-04-05 20:01:24.309358 create model matrix +#> 2024-04-05 20:03:16.483977 create model matrix #> #> rgstr_> head(registration_mod) #> registration_variableG0 registration_variableG1 registration_variableG2M @@ -224,14 +224,14 @@

    Examples

    #> A_G1 0 19.18719 #> #> rgst__> block_cor <- registration_block_cor(sce_pseudo, registration_mod) -#> 2024-04-05 20:01:24.320518 run duplicateCorrelation() -#> 2024-04-05 20:01:25.618793 The estimated correlation is: -0.0187869166526901 +#> 2024-04-05 20:03:16.49611 run duplicateCorrelation() +#> 2024-04-05 20:03:17.797159 The estimated correlation is: -0.0187869166526901 results_enrichment <- registration_stats_enrichment(sce_pseudo, block_cor, "age", gene_ensembl = "ensembl", gene_name = "gene_name" ) -#> 2024-04-05 20:01:25.622413 computing enrichment statistics -#> 2024-04-05 20:01:25.742697 extract and reformat enrichment results +#> 2024-04-05 20:03:17.800696 computing enrichment statistics +#> 2024-04-05 20:03:17.919357 extract and reformat enrichment results head(results_enrichment) #> t_stat_G0 t_stat_G1 t_stat_G2M t_stat_S p_value_G0 p_value_G1 #> Gene_0001 0.1482017 0.5610669 -0.3612235 -0.3458508 0.88374480 0.58130631 @@ -260,8 +260,8 @@

    Examples

    block_cor = NaN, "age", gene_ensembl = "ensembl", gene_name = "gene_name" ) -#> 2024-04-05 20:01:25.776383 computing enrichment statistics -#> 2024-04-05 20:01:25.880724 extract and reformat enrichment results +#> 2024-04-05 20:03:17.952387 computing enrichment statistics +#> 2024-04-05 20:03:18.055944 extract and reformat enrichment results head(results_enrichment_nan) #> t_stat_G0 t_stat_G1 t_stat_G2M t_stat_S p_value_G0 p_value_G1 #> Gene_0001 0.1497747 0.56711100 -0.3650801 -0.3495404 0.88252049 0.57727506 diff --git a/reference/registration_stats_pairwise.html b/reference/registration_stats_pairwise.html index dc782cf0..2c472e2a 100644 --- a/reference/registration_stats_pairwise.html +++ b/reference/registration_stats_pairwise.html @@ -173,9 +173,9 @@

    Examples

    #> #> rgstr_> ## Pseudo-bulk #> rgstr_> sce_pseudo <- registration_pseudobulk(sce, "Cell_Cycle", "sample_id", c("age"), min_ncells = NULL) -#> 2024-04-05 20:01:26.357244 make pseudobulk object -#> 2024-04-05 20:01:26.513061 drop lowly expressed genes -#> 2024-04-05 20:01:26.567246 normalize expression +#> 2024-04-05 20:03:18.533595 make pseudobulk object +#> 2024-04-05 20:03:18.695637 drop lowly expressed genes +#> 2024-04-05 20:03:18.751336 normalize expression #> #> rgstr_> colData(sce_pseudo) #> DataFrame with 20 rows and 8 columns @@ -207,7 +207,7 @@

    Examples

    #> E_S S E 11 #> #> rgstr_> registration_mod <- registration_model(sce_pseudo, "age") -#> 2024-04-05 20:01:26.641132 create model matrix +#> 2024-04-05 20:03:18.827435 create model matrix #> #> rgstr_> head(registration_mod) #> registration_variableG0 registration_variableG1 registration_variableG2M @@ -226,14 +226,14 @@

    Examples

    #> A_G1 0 19.18719 #> #> rgst__> block_cor <- registration_block_cor(sce_pseudo, registration_mod) -#> 2024-04-05 20:01:26.652237 run duplicateCorrelation() -#> 2024-04-05 20:01:27.948041 The estimated correlation is: -0.0187869166526901 +#> 2024-04-05 20:03:18.838534 run duplicateCorrelation() +#> 2024-04-05 20:03:20.129076 The estimated correlation is: -0.0187869166526901 results_pairwise <- registration_stats_pairwise(sce_pseudo, registration_mod, block_cor, gene_ensembl = "ensembl", gene_name = "gene_name" ) -#> 2024-04-05 20:01:27.950006 running the baseline pairwise model -#> 2024-04-05 20:01:27.96657 computing pairwise statistics +#> 2024-04-05 20:03:20.13099 running the baseline pairwise model +#> 2024-04-05 20:03:20.147259 computing pairwise statistics head(results_pairwise) #> t_stat_G0-G1 t_stat_G0-G2M t_stat_G0-S t_stat_G1-G2M t_stat_G1-S #> Gene_0001 -0.2393683 0.29771391 0.28880637 0.5370822 0.5281747 @@ -277,8 +277,8 @@

    Examples

    block_cor = NaN, gene_ensembl = "ensembl", gene_name = "gene_name" ) -#> 2024-04-05 20:01:28.03338 running the baseline pairwise model -#> 2024-04-05 20:01:28.051486 computing pairwise statistics +#> 2024-04-05 20:03:20.21355 running the baseline pairwise model +#> 2024-04-05 20:03:20.230973 computing pairwise statistics head(results_pairwise_nan) #> t_stat_G0-G1 t_stat_G0-G2M t_stat_G0-S t_stat_G1-G2M t_stat_G1-S #> Gene_0001 -0.2419770 0.30095840 0.29195379 0.5429354 0.5339308 diff --git a/reference/registration_wrapper.html b/reference/registration_wrapper.html index ceb90e1a..8539540e 100644 --- a/reference/registration_wrapper.html +++ b/reference/registration_wrapper.html @@ -200,18 +200,18 @@

    Examples

    sce, "Cell_Cycle", "sample_id", c("age"), "ensembl", "gene_name", "wrapper" ) -#> 2024-04-05 20:01:28.568415 make pseudobulk object -#> 2024-04-05 20:01:28.754401 dropping 9 pseudo-bulked samples that are below 'min_ncells'. -#> 2024-04-05 20:01:28.775645 drop lowly expressed genes -#> 2024-04-05 20:01:28.828816 normalize expression -#> 2024-04-05 20:01:28.885857 create model matrix -#> 2024-04-05 20:01:28.896152 run duplicateCorrelation() -#> 2024-04-05 20:01:31.332342 The estimated correlation is: -0.0783081238514532 -#> 2024-04-05 20:01:31.334621 computing enrichment statistics -#> 2024-04-05 20:01:31.486938 extract and reformat enrichment results -#> 2024-04-05 20:01:31.515873 running the baseline pairwise model -#> 2024-04-05 20:01:31.534001 computing pairwise statistics -#> 2024-04-05 20:01:31.60749 computing F-statistics +#> 2024-04-05 20:03:20.776905 make pseudobulk object +#> 2024-04-05 20:03:20.937428 dropping 9 pseudo-bulked samples that are below 'min_ncells'. +#> 2024-04-05 20:03:20.959517 drop lowly expressed genes +#> 2024-04-05 20:03:21.015265 normalize expression +#> 2024-04-05 20:03:21.073395 create model matrix +#> 2024-04-05 20:03:21.083679 run duplicateCorrelation() +#> 2024-04-05 20:03:23.527868 The estimated correlation is: -0.0783081238514532 +#> 2024-04-05 20:03:23.530216 computing enrichment statistics +#> 2024-04-05 20:03:23.686416 extract and reformat enrichment results +#> 2024-04-05 20:03:23.711984 running the baseline pairwise model +#> 2024-04-05 20:03:23.730237 computing pairwise statistics +#> 2024-04-05 20:03:23.80478 computing F-statistics diff --git a/reference/sce_to_spe.html b/reference/sce_to_spe.html index b85add1c..ae7ae9b5 100644 --- a/reference/sce_to_spe.html +++ b/reference/sce_to_spe.html @@ -127,7 +127,7 @@

    Examples

    ## Transform it to a SpatialExperiment object spe <- sce_to_spe(sce) } -#> 2024-04-05 20:01:33.193059 loading file /github/home/.cache/R/BiocFileCache/155f98a302_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-04-05 20:03:26.418618 loading file /github/home/.cache/R/BiocFileCache/1560561f15f7_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 diff --git a/reference/sig_genes_extract.html b/reference/sig_genes_extract.html index 57f3379e..8454427e 100644 --- a/reference/sig_genes_extract.html +++ b/reference/sig_genes_extract.html @@ -156,9 +156,9 @@

    Examples

    if (!exists("modeling_results")) { modeling_results <- fetch_data(type = "modeling_results") } -#> 2024-04-05 20:01:46.348571 loading file /github/home/.cache/R/BiocFileCache/11592b032277_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1 +#> 2024-04-05 20:03:40.14816 loading file /github/home/.cache/R/BiocFileCache/115b6b55de6b_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1 if (!exists("sce_layer")) sce_layer <- fetch_data(type = "sce_layer") -#> 2024-04-05 20:01:47.096632 loading file /github/home/.cache/R/BiocFileCache/11597ad98e84_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-04-05 20:03:41.339569 loading file /github/home/.cache/R/BiocFileCache/115b403d7ac1_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1 ## anova top 10 genes sig_genes_extract( diff --git a/reference/sig_genes_extract_all.html b/reference/sig_genes_extract_all.html index e7f5043d..ba73d558 100644 --- a/reference/sig_genes_extract_all.html +++ b/reference/sig_genes_extract_all.html @@ -128,9 +128,9 @@

    Examples

    if (!exists("modeling_results")) { modeling_results <- fetch_data(type = "modeling_results") } -#> 2024-04-05 20:01:50.81045 loading file /github/home/.cache/R/BiocFileCache/11592b032277_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1 +#> 2024-04-05 20:03:45.510109 loading file /github/home/.cache/R/BiocFileCache/115b6b55de6b_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1 if (!exists("sce_layer")) sce_layer <- fetch_data(type = "sce_layer") -#> 2024-04-05 20:01:51.680661 loading file /github/home/.cache/R/BiocFileCache/11597ad98e84_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-04-05 20:03:46.790189 loading file /github/home/.cache/R/BiocFileCache/115b403d7ac1_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1 ## top 10 genes for all models sig_genes_extract_all( diff --git a/reference/vis_clus.html b/reference/vis_clus.html index 009db651..256d8bd0 100644 --- a/reference/vis_clus.html +++ b/reference/vis_clus.html @@ -232,7 +232,7 @@

    Examples

    ) print(p4) } -#> 2024-04-05 20:01:53.933918 loading file /github/home/.cache/R/BiocFileCache/155f98a302_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-04-05 20:03:49.63713 loading file /github/home/.cache/R/BiocFileCache/1560561f15f7_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 diff --git a/reference/vis_clus_p.html b/reference/vis_clus_p.html index 3ffc6ea8..437c1a9d 100644 --- a/reference/vis_clus_p.html +++ b/reference/vis_clus_p.html @@ -202,7 +202,7 @@

    Examples

    ## Clean up rm(spe_sub) } -#> 2024-04-05 20:02:13.361915 loading file /github/home/.cache/R/BiocFileCache/155f98a302_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-04-05 20:04:09.759027 loading file /github/home/.cache/R/BiocFileCache/1560561f15f7_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 diff --git a/reference/vis_gene.html b/reference/vis_gene.html index f0a5b64c..2da5153d 100644 --- a/reference/vis_gene.html +++ b/reference/vis_gene.html @@ -331,7 +331,7 @@

    Examples

    ) print(p8) } -#> 2024-04-05 20:02:28.329119 loading file /github/home/.cache/R/BiocFileCache/155f98a302_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-04-05 20:04:25.311239 loading file /github/home/.cache/R/BiocFileCache/1560561f15f7_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 diff --git a/reference/vis_gene_p.html b/reference/vis_gene_p.html index 6e1b4236..54237d8f 100644 --- a/reference/vis_gene_p.html +++ b/reference/vis_gene_p.html @@ -220,7 +220,7 @@

    Examples

    ## Clean up rm(spe_sub) } -#> 2024-04-05 20:02:54.512688 loading file /github/home/.cache/R/BiocFileCache/155f98a302_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-04-05 20:04:51.962301 loading file /github/home/.cache/R/BiocFileCache/1560561f15f7_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 diff --git a/reference/vis_grid_clus.html b/reference/vis_grid_clus.html index c398728a..6b2bf2dd 100644 --- a/reference/vis_grid_clus.html +++ b/reference/vis_grid_clus.html @@ -227,7 +227,7 @@

    Examples

    ## for subject 3 cowplot::plot_grid(plotlist = p_list, ncol = 2) } -#> 2024-04-05 20:03:09.585646 loading file /github/home/.cache/R/BiocFileCache/155f98a302_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-04-05 20:05:07.528855 loading file /github/home/.cache/R/BiocFileCache/1560561f15f7_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 diff --git a/reference/vis_grid_gene.html b/reference/vis_grid_gene.html index bea8eb4d..9fd8ca56 100644 --- a/reference/vis_grid_gene.html +++ b/reference/vis_grid_gene.html @@ -246,7 +246,7 @@

    Examples

    ## for subject 3 cowplot::plot_grid(plotlist = p_list, ncol = 2) } -#> 2024-04-05 20:03:25.870071 loading file /github/home/.cache/R/BiocFileCache/155f98a302_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-04-05 20:05:24.595774 loading file /github/home/.cache/R/BiocFileCache/1560561f15f7_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1