From c78697c744032cc313585c7d3e84db3b24ce6000 Mon Sep 17 00:00:00 2001 From: lcolladotor Date: Thu, 12 Dec 2024 18:44:15 +0000 Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20LieberIn?= =?UTF-8?q?stitute/spatialLIBD@e9de73123c35f4f3407f3aa2f5596252b10c7634=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 ++++---- pkgdown.yml | 2 +- reference/add_images.html | 26 ++++++++--------- reference/add_key.html | 2 +- reference/add_qc_metrics.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 | 4 +-- 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, 138 insertions(+), 138 deletions(-) diff --git a/articles/TenX_data_download.html b/articles/TenX_data_download.html index 271d76c9..58bd1d3e 100644 --- a/articles/TenX_data_download.html +++ b/articles/TenX_data_download.html @@ -532,7 +532,7 @@

From Gencode## Show the GTF cache location gtf_cache #> BFC4 -#> "/github/home/.cache/R/BiocFileCache/380587f56f2_gencode.v32.annotation.gtf.gz" +#> "/github/home/.cache/R/BiocFileCache/3801c36c892_gencode.v32.annotation.gtf.gz" ## Import into R (takes ~1 min) gtf <- rtracklayer::import(gtf_cache) @@ -818,11 +818,11 @@

Wrapper functions= c("lowres", "hires", "detected", "aligned"), load = TRUE, reference_gtf = gtf_cache ) -#> 2024-12-12 18:40:45.704478 SpatialExperiment::read10xVisium: reading basic data from SpaceRanger -#> 2024-12-12 18:40:55.522243 read10xVisiumAnalysis: reading analysis output from SpaceRanger -#> 2024-12-12 18:40:56.532798 add10xVisiumAnalysis: adding analysis output from SpaceRanger -#> 2024-12-12 18:40:56.688569 rtracklayer::import: reading the reference GTF file -#> 2024-12-12 18:41:21.156013 adding gene information to the SPE object +#> 2024-12-12 18:43:24.262228 SpatialExperiment::read10xVisium: reading basic data from SpaceRanger +#> 2024-12-12 18:43:34.233449 read10xVisiumAnalysis: reading analysis output from SpaceRanger +#> 2024-12-12 18:43:35.255102 add10xVisiumAnalysis: adding analysis output from SpaceRanger +#> 2024-12-12 18:43:35.426512 rtracklayer::import: reading the reference GTF file +#> 2024-12-12 18:43:59.78269 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() @@ -830,7 +830,7 @@

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. -#> 2024-12-12 18:41:22.54559 adding information used by spatialLIBD +#> 2024-12-12 18:44:01.162821 adding information used by spatialLIBD 
 ## Run our shiny app
 if (interactive()) {
@@ -1114,9 +1114,9 @@ 
Reproducibilitylibrary("knitr")
 knit("TenX_data_download.Rmd", tangle = TRUE)

Date the vignette was generated.

-
#> [1] "2024-12-12 18:41:23 UTC"
+
#> [1] "2024-12-12 18:44:02 UTC"

Wallclock time spent generating the vignette.

-
#> Time difference of 1.614 mins
+
#> Time difference of 1.618 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 c738d4ea..dde6c92d 100644
--- a/articles/guide_to_spatial_registration.html
+++ b/articles/guide_to_spatial_registration.html
@@ -288,7 +288,7 @@ 
Spatial Reference
 ## get reference layer enrichment statistics
 layer_modeling_results <- fetch_data(type = "modeling_results")
-#> 2024-12-12 18:37:52.464756 loading file /github/home/.cache/R/BiocFileCache/3805b6c3903_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
+#> 2024-12-12 18:40:32.258698 loading file /github/home/.cache/R/BiocFileCache/3804f51b77a_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
@@ -391,18 +391,18 @@ 
Get Enrichment statistics
     gene_ensembl = "gene_id",
     gene_name = "gene_name"
 )
-#> 2024-12-12 18:38:00.149968 make pseudobulk object
-#> 2024-12-12 18:38:01.872701 dropping 13 pseudo-bulked samples that are below 'min_ncells'.
-#> 2024-12-12 18:38:01.923235 drop lowly expressed genes
-#> 2024-12-12 18:38:02.075261 normalize expression
-#> 2024-12-12 18:38:02.83433 create model matrix
-#> 2024-12-12 18:38:02.858624 run duplicateCorrelation()
-#> 2024-12-12 18:38:16.565188 The estimated correlation is: 0.138734774807097
-#> 2024-12-12 18:38:16.568187 computing enrichment statistics
-#> 2024-12-12 18:38:17.761273 extract and reformat enrichment results
-#> 2024-12-12 18:38:17.817051 running the baseline pairwise model
-#> 2024-12-12 18:38:17.990126 computing pairwise statistics
-#> 2024-12-12 18:38:19.318014 computing F-statistics

+#> 2024-12-12 18:40:40.038542 make pseudobulk object
+#> 2024-12-12 18:40:41.777686 dropping 13 pseudo-bulked samples that are below 'min_ncells'.
+#> 2024-12-12 18:40:41.822305 drop lowly expressed genes
+#> 2024-12-12 18:40:41.974082 normalize expression
+#> 2024-12-12 18:40:42.711172 create model matrix
+#> 2024-12-12 18:40:42.735229 run duplicateCorrelation()
+#> 2024-12-12 18:40:56.569668 The estimated correlation is: 0.138734774807097
+#> 2024-12-12 18:40:56.572397 computing enrichment statistics
+#> 2024-12-12 18:40:57.739095 extract and reformat enrichment results
+#> 2024-12-12 18:40:57.795048 running the baseline pairwise model
+#> 2024-12-12 18:40:57.96067 computing pairwise statistics
+#> 2024-12-12 18:40:59.317734 computing F-statistics

Extract Enrichment t-statistics @@ -576,9 +576,9 @@

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

Date the vignette was generated.

-
#> [1] "2024-12-12 18:38:23 UTC"
+
#> [1] "2024-12-12 18:41:03 UTC"

Wallclock time spent generating the vignette.

-
#> Time difference of 43.255 secs
+
#> Time difference of 43.365 secs

R session information.

#> ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
 #>  setting  value
diff --git a/articles/multi_gene_plots.html b/articles/multi_gene_plots.html
index b8e65f37..00845c11 100644
--- a/articles/multi_gene_plots.html
+++ b/articles/multi_gene_plots.html
@@ -195,9 +195,9 @@ 
Plotting One Gene
 modeling_results <- fetch_data(type = "modeling_results")
-#> 2024-12-12 18:38:46.621616 loading file /github/home/.cache/R/BiocFileCache/3805b6c3903_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
+#> 2024-12-12 18:41:26.179451 loading file /github/home/.cache/R/BiocFileCache/3804f51b77a_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
 sce_layer <- fetch_data(type = "sce_layer")
-#> 2024-12-12 18:38:47.509937 loading file /github/home/.cache/R/BiocFileCache/3806f39865b_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-12-12 18:41:27.013528 loading file /github/home/.cache/R/BiocFileCache/38072607a06_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
 sig_genes <- sig_genes_extract_all(
     n = 400,
     modeling_results = modeling_results,
@@ -421,9 +421,9 @@ 
Reproducibilitylibrary("knitr")
 knit("multi_gene_plots.Rmd", tangle = TRUE)

 
Date the vignette was generated.

-
#> [1] "2024-12-12 18:39:03 UTC"

+
#> [1] "2024-12-12 18:41:42 UTC"

 
Wallclock time spent generating the vignette.

-
#> Time difference of 35.751 secs

+
#> Time difference of 35.136 secs

 
R session information.

 
#> ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
 #>  setting  value
diff --git a/articles/spatialLIBD.html b/articles/spatialLIBD.html
index f6bdd316..5854b41c 100644
--- a/articles/spatialLIBD.html
+++ b/articles/spatialLIBD.html
@@ -414,7 +414,7 @@ 
Downloading the data with s
 
 ## Download the small example sce data
 sce <- fetch_data(type = "sce_example", eh = ehub)
-#> 2024-12-12 18:39:19.418456 loading file /github/home/.cache/R/BiocFileCache/380300534a4_sce_sub_for_vignette.Rdata%3Fdl%3D1
+#> 2024-12-12 18:41:58.168969 loading file /github/home/.cache/R/BiocFileCache/3801aadfd48_sce_sub_for_vignette.Rdata%3Fdl%3D1
 
 ## Convert to a SpatialExperiment object
 spe <- sce_to_spe(sce)
@@ -426,9 +426,9 @@ 
Downloading the data with s
 
 ## Query ExperimentHub and download the data
 if (!exists("sce_layer")) sce_layer <- fetch_data(type = "sce_layer", eh = ehub)
-#> 2024-12-12 18:39:23.516332 loading file /github/home/.cache/R/BiocFileCache/3806f39865b_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-12-12 18:42:02.240913 loading file /github/home/.cache/R/BiocFileCache/38072607a06_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
 modeling_results <- fetch_data("modeling_results", eh = ehub)
-#> 2024-12-12 18:39:23.939804 loading file /github/home/.cache/R/BiocFileCache/3805b6c3903_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1

+#> 2024-12-12 18:42:02.65302 loading file /github/home/.cache/R/BiocFileCache/3804f51b77a_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1

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

 
@@ -501,7 +501,7 @@ 
Downloading the data with s
         )
 )
 #>    user  system elapsed 
-#>   9.446   0.408   9.884
+#>   9.371   0.348   9.743
 
 ## Explore the result
 class(sig_genes)
@@ -1380,9 +1380,9 @@ 
Reproducibilitylibrary("knitr")
 knit("spatialLIBD.Rmd", tangle = TRUE)

 
Date the vignette was generated.

-
#> [1] "2024-12-12 18:39:42 UTC"

+
#> [1] "2024-12-12 18:42:20 UTC"

 
Wallclock time spent generating the vignette.

-
#> Time difference of 35.478 secs

+
#> Time difference of 34.805 secs

 
R session information.

 
#> ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
 #>  setting  value
diff --git a/pkgdown.yml b/pkgdown.yml
index 07617d59..21e793a8 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -6,4 +6,4 @@ articles:
   multi_gene_plots: multi_gene_plots.html
   spatialLIBD: spatialLIBD.html
   TenX_data_download: TenX_data_download.html
-last_built: 2024-12-12T18:33Z
+last_built: 2024-12-12T18:36Z
diff --git a/reference/add_images.html b/reference/add_images.html
index 1b2acb8f..c83deba7 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")
     ))
 }
-#> 2024-12-12 18:33:43.773041 loading file /github/home/.cache/R/BiocFileCache/df8125c9b90_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
-#> 2024-12-12 18:33:54.346232 adding image for sample 151507
-#> 2024-12-12 18:33:54.994709 adding image for sample 151508
+#> 2024-12-12 18:36:20.738189 loading file /github/home/.cache/R/BiocFileCache/df71cd93aff_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-12-12 18:36:31.498702 adding image for sample 151507
+#> 2024-12-12 18:36:32.184158 adding image for sample 151508
 #> Warning: No image was found for sample: 151508
-#> 2024-12-12 18:33:54.995429 adding image for sample 151509
+#> 2024-12-12 18:36:32.184891 adding image for sample 151509
 #> Warning: No image was found for sample: 151509
-#> 2024-12-12 18:33:54.995955 adding image for sample 151510
+#> 2024-12-12 18:36:32.185403 adding image for sample 151510
 #> Warning: No image was found for sample: 151510
-#> 2024-12-12 18:33:54.996433 adding image for sample 151669
+#> 2024-12-12 18:36:32.185881 adding image for sample 151669
 #> Warning: No image was found for sample: 151669
-#> 2024-12-12 18:33:54.9969 adding image for sample 151670
+#> 2024-12-12 18:36:32.186352 adding image for sample 151670
 #> Warning: No image was found for sample: 151670
-#> 2024-12-12 18:33:54.997356 adding image for sample 151671
+#> 2024-12-12 18:36:32.186826 adding image for sample 151671
 #> Warning: No image was found for sample: 151671
-#> 2024-12-12 18:33:54.997815 adding image for sample 151672
+#> 2024-12-12 18:36:32.187293 adding image for sample 151672
 #> Warning: No image was found for sample: 151672
-#> 2024-12-12 18:33:54.998266 adding image for sample 151673
+#> 2024-12-12 18:36:32.187801 adding image for sample 151673
 #> Warning: No image was found for sample: 151673
-#> 2024-12-12 18:33:54.998709 adding image for sample 151674
+#> 2024-12-12 18:36:32.18826 adding image for sample 151674
 #> Warning: No image was found for sample: 151674
-#> 2024-12-12 18:33:54.999151 adding image for sample 151675
+#> 2024-12-12 18:36:32.188714 adding image for sample 151675
 #> Warning: No image was found for sample: 151675
-#> 2024-12-12 18:33:54.999647 adding image for sample 151676
+#> 2024-12-12 18:36:32.189166 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 7d75a6ea..4b3d6896 100644
--- a/reference/add_key.html
+++ b/reference/add_key.html
@@ -124,7 +124,7 @@ 
Examples

     spe$key_original <- NULL
     head(spe$key)
 }
-#> 2024-12-12 18:33:57.220629 loading file /github/home/.cache/R/BiocFileCache/df8125c9b90_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-12-12 18:36:34.406131 loading file /github/home/.cache/R/BiocFileCache/df71cd93aff_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
 #> [1] "151507_AAACAACGAATAGTTC-1" "151507_AAACAAGTATCTCCCA-1"
 #> [3] "151507_AAACAATCTACTAGCA-1" "151507_AAACACCAATAACTGC-1"
 #> [5] "151507_AAACAGCTTTCAGAAG-1" "151507_AAACAGGGTCTATATT-1"
diff --git a/reference/add_qc_metrics.html b/reference/add_qc_metrics.html
index 483f2503..5d9baa98 100644
--- a/reference/add_qc_metrics.html
+++ b/reference/add_qc_metrics.html
@@ -144,7 +144,7 @@ 
Author

     
Examples

     
## Obtain the necessary data
 spe_pre_qc <- fetch_data("spatialDLPFC_Visium_example_subset")
-#> 2024-12-12 18:34:07.763307 loading file /github/home/.cache/R/BiocFileCache/380817be54_spatialDLPFC_spe_subset_example.rds%3Fdl%3D1
+#> 2024-12-12 18:36:45.058894 loading file /github/home/.cache/R/BiocFileCache/3801440830e_spatialDLPFC_spe_subset_example.rds%3Fdl%3D1
 
 ## For now, we fake out tissue spots in example data
 spe_qc <- spe_pre_qc
diff --git a/reference/annotate_registered_clusters.html b/reference/annotate_registered_clusters.html
index 64847c13..b74b9f53 100644
--- a/reference/annotate_registered_clusters.html
+++ b/reference/annotate_registered_clusters.html
@@ -137,7 +137,7 @@ 
Examples

 if (!exists("modeling_results")) {
     modeling_results <- fetch_data(type = "modeling_results")
 }
-#> 2024-12-12 18:34:19.317689 loading file /github/home/.cache/R/BiocFileCache/3805b6c3903_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
+#> 2024-12-12 18:36:56.537035 loading file /github/home/.cache/R/BiocFileCache/3804f51b77a_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 0f0d9231..272aeb9f 100644
--- a/reference/check_modeling_results.html
+++ b/reference/check_modeling_results.html
@@ -109,7 +109,7 @@ 
Examples

 if (!exists("modeling_results")) {
     modeling_results <- fetch_data(type = "modeling_results")
 }
-#> 2024-12-12 18:34:20.266893 loading file /github/home/.cache/R/BiocFileCache/3805b6c3903_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
+#> 2024-12-12 18:36:57.500987 loading file /github/home/.cache/R/BiocFileCache/3804f51b77a_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 faa4a9f1..5d94dca1 100644
--- a/reference/check_sce.html
+++ b/reference/check_sce.html
@@ -131,7 +131,7 @@ 
Examples

     ## Check the object
     check_sce(sce_example)
 }
-#> 2024-12-12 18:34:21.153916 loading file /github/home/.cache/R/BiocFileCache/380300534a4_sce_sub_for_vignette.Rdata%3Fdl%3D1
+#> 2024-12-12 18:36:58.403451 loading file /github/home/.cache/R/BiocFileCache/3801aadfd48_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 548ab065..c19161e6 100644
--- a/reference/check_sce_layer.html
+++ b/reference/check_sce_layer.html
@@ -112,7 +112,7 @@ 
Examples

 ## Obtain example data from the HumanPilot project
 ## (Maynard, Collado-Torres, et al, 2021)
 if (!exists("sce_layer")) sce_layer <- fetch_data("sce_layer")
-#> 2024-12-12 18:34:23.248007 loading file /github/home/.cache/R/BiocFileCache/3806f39865b_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-12-12 18:37:00.494189 loading file /github/home/.cache/R/BiocFileCache/38072607a06_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
 
 ## Check the pseudo-bulked data
 check_sce_layer(sce_layer)
diff --git a/reference/check_spe.html b/reference/check_spe.html
index cd02ef68..5c711358 100644
--- a/reference/check_spe.html
+++ b/reference/check_spe.html
@@ -123,7 +123,7 @@ 
Examples

     ## Check the object
     check_spe(spe)
 }
-#> 2024-12-12 18:34:24.264538 loading file /github/home/.cache/R/BiocFileCache/df8125c9b90_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-12-12 18:37:01.528716 loading file /github/home/.cache/R/BiocFileCache/df71cd93aff_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 e3853539..208d6893 100644
--- a/reference/cluster_export.html
+++ b/reference/cluster_export.html
@@ -134,7 +134,7 @@ 
Examples

     cluster_export(spe, "spatialLIBD")
     cluster_export(spe, "GraphBased")
 }
-#> 2024-12-12 18:34:33.317536 loading file /github/home/.cache/R/BiocFileCache/df8125c9b90_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-12-12 18:37:10.660946 loading file /github/home/.cache/R/BiocFileCache/df71cd93aff_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 07b624ef..a23810e5 100644
--- a/reference/cluster_import.html
+++ b/reference/cluster_import.html
@@ -137,11 +137,11 @@ 
Examples

     ## Re-import them
     colData(cluster_import(spe))
 }
-#> 2024-12-12 18:34:43.486599 loading file /github/home/.cache/R/BiocFileCache/df8125c9b90_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-12-12 18:37:21.035271 loading file /github/home/.cache/R/BiocFileCache/df71cd93aff_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
 #> Overwriting 'spe$key'. Set 'overwrite = FALSE' if you do not want to overwrite it.
-#> Warning: '/tmp/RtmpnmGO7d/exported_clusters/spatialLIBD' already exists
+#> Warning: '/tmp/Rtmp6TAWFo/exported_clusters/spatialLIBD' already exists
 #> Overwriting 'spe$key'. Set 'overwrite = FALSE' if you do not want to overwrite it.
-#> Warning: '/tmp/RtmpnmGO7d/exported_clusters/GraphBased' already exists
+#> Warning: '/tmp/Rtmp6TAWFo/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 5c9aa14d..68da6ff5 100644
--- a/reference/fetch_data.html
+++ b/reference/fetch_data.html
@@ -166,7 +166,7 @@ 
Examples

 ## Download the SingleCellExperiment object
 ## at the layer-level
 if (!exists("sce_layer")) sce_layer <- fetch_data("sce_layer")
-#> 2024-12-12 18:34:54.306992 loading file /github/home/.cache/R/BiocFileCache/3806f39865b_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-12-12 18:37:32.030823 loading file /github/home/.cache/R/BiocFileCache/38072607a06_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 9e3b0011..90884937 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")
 }
-#> 2024-12-12 18:34:55.758459 loading file /github/home/.cache/R/BiocFileCache/df8125c9b90_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-12-12 18:37:33.448849 loading file /github/home/.cache/R/BiocFileCache/df71cd93aff_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 e51a9405..4b387cc7 100644
--- a/reference/gene_set_enrichment.html
+++ b/reference/gene_set_enrichment.html
@@ -177,7 +177,7 @@ 
Examples

 if (!exists("modeling_results")) {
     modeling_results <- fetch_data(type = "modeling_results")
 }
-#> 2024-12-12 18:35:05.012936 loading file /github/home/.cache/R/BiocFileCache/3805b6c3903_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
+#> 2024-12-12 18:37:42.696556 loading file /github/home/.cache/R/BiocFileCache/3804f51b77a_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 7a3d5e66..6ac3bbe9 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")
 }
-#> 2024-12-12 18:35:06.139526 loading file /github/home/.cache/R/BiocFileCache/3805b6c3903_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
+#> 2024-12-12 18:37:43.818419 loading file /github/home/.cache/R/BiocFileCache/3804f51b77a_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 bfd4e164..f20ad85d 100644
--- a/reference/geom_spatial.html
+++ b/reference/geom_spatial.html
@@ -175,7 +175,7 @@ 
Examples

     ## Clean up
     rm(spe_sub)
 }
-#> 2024-12-12 18:35:07.692151 loading file /github/home/.cache/R/BiocFileCache/df8125c9b90_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-12-12 18:37:45.344296 loading file /github/home/.cache/R/BiocFileCache/df71cd93aff_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
 
 

     
diff --git a/reference/get_colors.html b/reference/get_colors.html
index afb4db0d..d1628625 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")
-#> 2024-12-12 18:35:17.650777 loading file /github/home/.cache/R/BiocFileCache/3806f39865b_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-12-12 18:37:55.353127 loading file /github/home/.cache/R/BiocFileCache/38072607a06_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 af3468a4..87696386 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)
 }
-#> 2024-12-12 18:35:18.677344 loading file /github/home/.cache/R/BiocFileCache/df8125c9b90_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-12-12 18:37:56.390668 loading file /github/home/.cache/R/BiocFileCache/df71cd93aff_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
 
 

     
diff --git a/reference/img_update.html b/reference/img_update.html
index eaee5018..9a107b5e 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))
 }
-#> 2024-12-12 18:35:29.053636 loading file /github/home/.cache/R/BiocFileCache/df8125c9b90_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-12-12 18:38:07.93355 loading file /github/home/.cache/R/BiocFileCache/df71cd93aff_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 f13e2ab7..7834d5f2 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))
 }
-#> 2024-12-12 18:35:38.211438 loading file /github/home/.cache/R/BiocFileCache/df8125c9b90_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-12-12 18:38:17.179145 loading file /github/home/.cache/R/BiocFileCache/df71cd93aff_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 d97449a5..888522aa 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")
 }
-#> 2024-12-12 18:35:49.888485 loading file /github/home/.cache/R/BiocFileCache/3805b6c3903_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
+#> 2024-12-12 18:38:28.987618 loading file /github/home/.cache/R/BiocFileCache/3804f51b77a_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
 if (!exists("sce_layer")) sce_layer <- fetch_data(type = "sce_layer")
-#> 2024-12-12 18:35:50.668504 loading file /github/home/.cache/R/BiocFileCache/3806f39865b_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-12-12 18:38:29.797868 loading file /github/home/.cache/R/BiocFileCache/38072607a06_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 439e04bb..7a7ebc0a 100644
--- a/reference/layer_stat_cor.html
+++ b/reference/layer_stat_cor.html
@@ -161,7 +161,7 @@ 
Examples

 if (!exists("modeling_results")) {
     modeling_results <- fetch_data(type = "modeling_results")
 }
-#> 2024-12-12 18:35:53.356793 loading file /github/home/.cache/R/BiocFileCache/3805b6c3903_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
+#> 2024-12-12 18:38:32.565828 loading file /github/home/.cache/R/BiocFileCache/3804f51b77a_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 ad21c954..9ea1e7ee 100644
--- a/reference/layer_stat_cor_plot.html
+++ b/reference/layer_stat_cor_plot.html
@@ -168,13 +168,13 @@ 
Examples

 if (!exists("modeling_results")) {
     modeling_results <- fetch_data(type = "modeling_results")
 }
-#> 2024-12-12 18:35:54.434552 loading file /github/home/.cache/R/BiocFileCache/3805b6c3903_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
+#> 2024-12-12 18:38:33.630915 loading file /github/home/.cache/R/BiocFileCache/3804f51b77a_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
 
 ## query spatialDLPFC modeling results
 query_modeling_results <- fetch_data(
     type = "spatialDLPFC_Visium_modeling_results"
 )
-#> 2024-12-12 18:35:55.21739 loading file /github/home/.cache/R/BiocFileCache/df8cbfa14_modeling_results_BayesSpace_k09.Rdata%3Fdl%3D1
+#> 2024-12-12 18:38:34.528462 loading file /github/home/.cache/R/BiocFileCache/df7373191bc_modeling_results_BayesSpace_k09.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 45213532..821f8b50 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)
-#> 2024-12-12 18:36:02.693557 make pseudobulk object
-#> 2024-12-12 18:36:02.820699 drop lowly expressed genes
-#> 2024-12-12 18:36:02.889369 normalize expression
+#> 2024-12-12 18:38:41.984267 make pseudobulk object
+#> 2024-12-12 18:38:42.108331 drop lowly expressed genes
+#> 2024-12-12 18:38:42.168886 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")
-#> 2024-12-12 18:36:02.972162 create model matrix
+#> 2024-12-12 18:38:42.247758 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)
-#> 2024-12-12 18:36:02.985329 run duplicateCorrelation()
-#> 2024-12-12 18:36:04.301385 The estimated correlation is: -0.0187869166526901
+#> 2024-12-12 18:38:42.260323 run duplicateCorrelation()
+#> 2024-12-12 18:38:43.552145 The estimated correlation is: -0.0187869166526901
diff --git a/reference/registration_model.html b/reference/registration_model.html index 68268872..238ea3cb 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) -#> 2024-12-12 18:36:04.611733 make pseudobulk object -#> 2024-12-12 18:36:04.742464 drop lowly expressed genes -#> 2024-12-12 18:36:04.790202 normalize expression +#> 2024-12-12 18:38:43.860326 make pseudobulk object +#> 2024-12-12 18:38:43.992193 drop lowly expressed genes +#> 2024-12-12 18:38:44.03864 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") -#> 2024-12-12 18:36:04.874767 create model matrix +#> 2024-12-12 18:38:44.114175 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 502e81ce..0cfe0ed2 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) -#> 2024-12-12 18:36:05.230003 make pseudobulk object -#> 2024-12-12 18:36:05.329811 drop lowly expressed genes -#> 2024-12-12 18:36:05.376228 normalize expression +#> 2024-12-12 18:38:44.462835 make pseudobulk object +#> 2024-12-12 18:38:44.560726 drop lowly expressed genes +#> 2024-12-12 18:38:44.607114 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 61432d30..5746d581 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) -#> 2024-12-12 18:36:05.878278 make pseudobulk object -#> 2024-12-12 18:36:05.978312 drop lowly expressed genes -#> 2024-12-12 18:36:06.024745 normalize expression +#> 2024-12-12 18:38:45.105683 make pseudobulk object +#> 2024-12-12 18:38:45.203821 drop lowly expressed genes +#> 2024-12-12 18:38:45.25013 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") -#> 2024-12-12 18:36:06.102632 create model matrix +#> 2024-12-12 18:38:45.326164 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) -#> 2024-12-12 18:36:06.114175 run duplicateCorrelation() -#> 2024-12-12 18:36:07.422661 The estimated correlation is: -0.0187869166526901 +#> 2024-12-12 18:38:45.337741 run duplicateCorrelation() +#> 2024-12-12 18:38:46.631059 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" ) -#> 2024-12-12 18:36:07.43498 computing F-statistics +#> 2024-12-12 18:38:46.64308 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" ) -#> 2024-12-12 18:36:07.496944 computing F-statistics +#> 2024-12-12 18:38:46.704501 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" ) -#> 2024-12-12 18:36:07.546639 computing F-statistics +#> 2024-12-12 18:38:46.753834 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 6ab9e51d..b4a39d78 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) -#> 2024-12-12 18:36:07.988426 make pseudobulk object -#> 2024-12-12 18:36:08.089936 drop lowly expressed genes -#> 2024-12-12 18:36:08.136602 normalize expression +#> 2024-12-12 18:38:47.188352 make pseudobulk object +#> 2024-12-12 18:38:47.286896 drop lowly expressed genes +#> 2024-12-12 18:38:47.333005 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") -#> 2024-12-12 18:36:08.211847 create model matrix +#> 2024-12-12 18:38:47.407834 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) -#> 2024-12-12 18:36:08.223509 run duplicateCorrelation() -#> 2024-12-12 18:36:09.535232 The estimated correlation is: -0.0187869166526901 +#> 2024-12-12 18:38:47.419312 run duplicateCorrelation() +#> 2024-12-12 18:38:48.712227 The estimated correlation is: -0.0187869166526901 results_enrichment <- registration_stats_enrichment(sce_pseudo, block_cor, "age", gene_ensembl = "ensembl", gene_name = "gene_name" ) -#> 2024-12-12 18:36:09.538872 computing enrichment statistics -#> 2024-12-12 18:36:09.660229 extract and reformat enrichment results +#> 2024-12-12 18:38:48.715665 computing enrichment statistics +#> 2024-12-12 18:38:48.833175 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" ) -#> 2024-12-12 18:36:09.693325 computing enrichment statistics -#> 2024-12-12 18:36:09.794971 extract and reformat enrichment results +#> 2024-12-12 18:38:48.865673 computing enrichment statistics +#> 2024-12-12 18:38:48.96927 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 647c3b0b..1cdff5c0 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) -#> 2024-12-12 18:36:10.161558 make pseudobulk object -#> 2024-12-12 18:36:10.260281 drop lowly expressed genes -#> 2024-12-12 18:36:10.306612 normalize expression +#> 2024-12-12 18:38:49.332263 make pseudobulk object +#> 2024-12-12 18:38:49.431088 drop lowly expressed genes +#> 2024-12-12 18:38:49.477803 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") -#> 2024-12-12 18:36:10.382539 create model matrix +#> 2024-12-12 18:38:49.553601 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) -#> 2024-12-12 18:36:10.394083 run duplicateCorrelation() -#> 2024-12-12 18:36:11.765182 The estimated correlation is: -0.0187869166526901 +#> 2024-12-12 18:38:49.565056 run duplicateCorrelation() +#> 2024-12-12 18:38:50.931537 The estimated correlation is: -0.0187869166526901 results_pairwise <- registration_stats_pairwise(sce_pseudo, registration_mod, block_cor, gene_ensembl = "ensembl", gene_name = "gene_name" ) -#> 2024-12-12 18:36:11.766948 running the baseline pairwise model -#> 2024-12-12 18:36:11.783901 computing pairwise statistics +#> 2024-12-12 18:38:50.933621 running the baseline pairwise model +#> 2024-12-12 18:38:50.950248 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" ) -#> 2024-12-12 18:36:11.849046 running the baseline pairwise model -#> 2024-12-12 18:36:11.866572 computing pairwise statistics +#> 2024-12-12 18:38:51.015594 running the baseline pairwise model +#> 2024-12-12 18:38:51.033027 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 df4c52ce..06c9d307 100644 --- a/reference/registration_wrapper.html +++ b/reference/registration_wrapper.html @@ -205,18 +205,18 @@

Examples

gene_name = "gene_name", suffix = "wrapper" ) -#> 2024-12-12 18:36:12.28755 make pseudobulk object -#> 2024-12-12 18:36:12.385776 dropping 9 pseudo-bulked samples that are below 'min_ncells'. -#> 2024-12-12 18:36:12.399431 drop lowly expressed genes -#> 2024-12-12 18:36:12.446355 normalize expression -#> 2024-12-12 18:36:12.504176 create model matrix -#> 2024-12-12 18:36:12.51492 run duplicateCorrelation() -#> 2024-12-12 18:36:14.913137 The estimated correlation is: -0.0783081238514531 -#> 2024-12-12 18:36:14.915789 computing enrichment statistics -#> 2024-12-12 18:36:15.033572 extract and reformat enrichment results -#> 2024-12-12 18:36:15.059526 running the baseline pairwise model -#> 2024-12-12 18:36:15.077892 computing pairwise statistics -#> 2024-12-12 18:36:15.154603 computing F-statistics +#> 2024-12-12 18:38:51.449238 make pseudobulk object +#> 2024-12-12 18:38:51.547856 dropping 9 pseudo-bulked samples that are below 'min_ncells'. +#> 2024-12-12 18:38:51.561445 drop lowly expressed genes +#> 2024-12-12 18:38:51.608139 normalize expression +#> 2024-12-12 18:38:51.666588 create model matrix +#> 2024-12-12 18:38:51.677382 run duplicateCorrelation() +#> 2024-12-12 18:38:54.045074 The estimated correlation is: -0.0783081238514531 +#> 2024-12-12 18:38:54.047661 computing enrichment statistics +#> 2024-12-12 18:38:54.164009 extract and reformat enrichment results +#> 2024-12-12 18:38:54.189076 running the baseline pairwise model +#> 2024-12-12 18:38:54.212286 computing pairwise statistics +#> 2024-12-12 18:38:54.287149 computing F-statistics ## Explore the results from registration_wrapper() class(example_modeling_results) diff --git a/reference/sce_to_spe.html b/reference/sce_to_spe.html index 0011ec15..068229a3 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) } -#> 2024-12-12 18:36:16.89109 loading file /github/home/.cache/R/BiocFileCache/df8125c9b90_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-12-12 18:38:55.940567 loading file /github/home/.cache/R/BiocFileCache/df71cd93aff_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 fc59b526..6ab7843b 100644 --- a/reference/sig_genes_extract.html +++ b/reference/sig_genes_extract.html @@ -157,9 +157,9 @@

Examples

if (!exists("modeling_results")) { modeling_results <- fetch_data(type = "modeling_results") } -#> 2024-12-12 18:36:24.912731 loading file /github/home/.cache/R/BiocFileCache/3805b6c3903_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1 +#> 2024-12-12 18:39:04.105216 loading file /github/home/.cache/R/BiocFileCache/3804f51b77a_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1 if (!exists("sce_layer")) sce_layer <- fetch_data(type = "sce_layer") -#> 2024-12-12 18:36:25.722782 loading file /github/home/.cache/R/BiocFileCache/3806f39865b_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-12-12 18:39:04.919025 loading file /github/home/.cache/R/BiocFileCache/38072607a06_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 e0dfc1b4..09bee127 100644 --- a/reference/sig_genes_extract_all.html +++ b/reference/sig_genes_extract_all.html @@ -129,9 +129,9 @@

Examples

if (!exists("modeling_results")) { modeling_results <- fetch_data(type = "modeling_results") } -#> 2024-12-12 18:36:27.722805 loading file /github/home/.cache/R/BiocFileCache/3805b6c3903_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1 +#> 2024-12-12 18:39:06.92331 loading file /github/home/.cache/R/BiocFileCache/3804f51b77a_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1 if (!exists("sce_layer")) sce_layer <- fetch_data(type = "sce_layer") -#> 2024-12-12 18:36:28.510094 loading file /github/home/.cache/R/BiocFileCache/3806f39865b_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-12-12 18:39:07.726227 loading file /github/home/.cache/R/BiocFileCache/38072607a06_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 8aaa8ea1..f582b133 100644 --- a/reference/vis_clus.html +++ b/reference/vis_clus.html @@ -242,7 +242,7 @@

Examples

) print(p4) } -#> 2024-12-12 18:36:31.540914 loading file /github/home/.cache/R/BiocFileCache/df8125c9b90_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-12-12 18:39:10.797729 loading file /github/home/.cache/R/BiocFileCache/df71cd93aff_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 d62487f3..629458a4 100644 --- a/reference/vis_clus_p.html +++ b/reference/vis_clus_p.html @@ -202,7 +202,7 @@

Examples

## Clean up rm(spe_sub) } -#> 2024-12-12 18:36:44.169538 loading file /github/home/.cache/R/BiocFileCache/df8125c9b90_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-12-12 18:39:23.64242 loading file /github/home/.cache/R/BiocFileCache/df71cd93aff_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 diff --git a/reference/vis_gene.html b/reference/vis_gene.html index 80a77f55..8799cda7 100644 --- a/reference/vis_gene.html +++ b/reference/vis_gene.html @@ -341,7 +341,7 @@

Examples

) print(p8) } -#> 2024-12-12 18:36:52.839072 loading file /github/home/.cache/R/BiocFileCache/df8125c9b90_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-12-12 18:39:32.455708 loading file /github/home/.cache/R/BiocFileCache/df71cd93aff_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 e53413af..35394857 100644 --- a/reference/vis_gene_p.html +++ b/reference/vis_gene_p.html @@ -215,7 +215,7 @@

Examples

## Clean up rm(spe_sub) } -#> 2024-12-12 18:37:10.200654 loading file /github/home/.cache/R/BiocFileCache/df8125c9b90_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-12-12 18:39:49.975443 loading file /github/home/.cache/R/BiocFileCache/df71cd93aff_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 a4d7e5ec..46e12867 100644 --- a/reference/vis_grid_clus.html +++ b/reference/vis_grid_clus.html @@ -237,7 +237,7 @@

Examples

## for subject 3 cowplot::plot_grid(plotlist = p_list, ncol = 2) } -#> 2024-12-12 18:37:19.720583 loading file /github/home/.cache/R/BiocFileCache/df8125c9b90_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-12-12 18:39:59.574238 loading file /github/home/.cache/R/BiocFileCache/df71cd93aff_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 d8a62295..a4bcb4fc 100644 --- a/reference/vis_grid_gene.html +++ b/reference/vis_grid_gene.html @@ -256,7 +256,7 @@

Examples

## for subject 3 cowplot::plot_grid(plotlist = p_list, ncol = 2) } -#> 2024-12-12 18:37:30.614748 loading file /github/home/.cache/R/BiocFileCache/df8125c9b90_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-12-12 18:40:10.478118 loading file /github/home/.cache/R/BiocFileCache/df71cd93aff_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1