diff --git a/articles/TenX_data_download.html b/articles/TenX_data_download.html index ea144684..bb8573ea 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/29a341ccbf3_gencode.v32.annotation.gtf.gz" +#> "/github/home/.cache/R/BiocFileCache/2996b35cfc2_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 ) -#> 2024-07-19 16:15:59.611155 SpatialExperiment::read10xVisium: reading basic data from SpaceRanger -#> 2024-07-19 16:16:11.118014 read10xVisiumAnalysis: reading analysis output from SpaceRanger -#> 2024-07-19 16:16:11.222624 add10xVisiumAnalysis: adding analysis output from SpaceRanger -#> 2024-07-19 16:16:11.466511 rtracklayer::import: reading the reference GTF file -#> 2024-07-19 16:16:38.948396 adding gene information to the SPE object +#> 2024-07-19 16:17:19.724118 SpatialExperiment::read10xVisium: reading basic data from SpaceRanger +#> 2024-07-19 16:17:31.044816 read10xVisiumAnalysis: reading analysis output from SpaceRanger +#> 2024-07-19 16:17:31.150279 add10xVisiumAnalysis: adding analysis output from SpaceRanger +#> 2024-07-19 16:17:31.394413 rtracklayer::import: reading the reference GTF file +#> 2024-07-19 16:17:58.71825 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. -#> 2024-07-19 16:16:39.203504 adding information used by spatialLIBD +#> 2024-07-19 16:17:58.969712 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] "2024-07-19 16:16:40 UTC"
+
#> [1] "2024-07-19 16:18:00 UTC"

Wallclock time spent generating the vignette.

-
#> Time difference of 1.684 mins
+
#> Time difference of 1.669 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 0ebbd284..62d3a43d 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")
-#> 2024-07-19 16:13:06.649509 loading file /github/home/.cache/R/BiocFileCache/29a6df9f139_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
+#> 2024-07-19 16:14:27.519916 loading file /github/home/.cache/R/BiocFileCache/2993f4cc32e_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"
 )
-#> 2024-07-19 16:13:14.445509 make pseudobulk object
-#> 2024-07-19 16:13:16.139074 dropping 13 pseudo-bulked samples that are below 'min_ncells'.
-#> 2024-07-19 16:13:16.198582 drop lowly expressed genes
-#> 2024-07-19 16:13:16.366075 normalize expression
-#> 2024-07-19 16:13:17.871261 create model matrix
-#> 2024-07-19 16:13:17.894957 run duplicateCorrelation()
-#> 2024-07-19 16:13:31.06397 The estimated correlation is: 0.138734774807097
-#> 2024-07-19 16:13:31.06644 computing enrichment statistics
-#> 2024-07-19 16:13:32.193383 extract and reformat enrichment results
-#> 2024-07-19 16:13:32.248189 running the baseline pairwise model
-#> 2024-07-19 16:13:32.412747 computing pairwise statistics
-#> 2024-07-19 16:13:33.763915 computing F-statistics

+#> 2024-07-19 16:14:35.293477 make pseudobulk object
+#> 2024-07-19 16:14:37.026498 dropping 13 pseudo-bulked samples that are below 'min_ncells'.
+#> 2024-07-19 16:14:37.085348 drop lowly expressed genes
+#> 2024-07-19 16:14:37.256214 normalize expression
+#> 2024-07-19 16:14:38.730633 create model matrix
+#> 2024-07-19 16:14:38.754426 run duplicateCorrelation()
+#> 2024-07-19 16:14:51.942116 The estimated correlation is: 0.138734774807097
+#> 2024-07-19 16:14:51.94471 computing enrichment statistics
+#> 2024-07-19 16:14:53.112203 extract and reformat enrichment results
+#> 2024-07-19 16:14:53.16769 running the baseline pairwise model
+#> 2024-07-19 16:14:53.337637 computing pairwise statistics
+#> 2024-07-19 16:14:54.682635 computing F-statistics

Extract Enrichment t-statistics @@ -562,9 +562,9 @@

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

Date the vignette was generated.

-
#> [1] "2024-07-19 16:13:35 UTC"
+
#> [1] "2024-07-19 16:14:56 UTC"

Wallclock time spent generating the vignette.

-
#> Time difference of 40.861 secs
+
#> Time difference of 40.834 secs

R session information.

#> ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
 #>  setting  value
diff --git a/articles/multi_gene_plots.html b/articles/multi_gene_plots.html
index 4d2ecf76..f4d2c6f1 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")
-#> 2024-07-19 16:13:59.844049 loading file /github/home/.cache/R/BiocFileCache/29a6df9f139_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
+#> 2024-07-19 16:15:20.502355 loading file /github/home/.cache/R/BiocFileCache/2993f4cc32e_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
 sce_layer <- fetch_data(type = "sce_layer")
-#> 2024-07-19 16:14:00.661599 loading file /github/home/.cache/R/BiocFileCache/29a67699111_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-07-19 16:15:21.302338 loading file /github/home/.cache/R/BiocFileCache/2993b875f9c_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] "2024-07-19 16:14:16 UTC"

+
#> [1] "2024-07-19 16:15:37 UTC"

 
Wallclock time spent generating the vignette.

-
#> Time difference of 36.497 secs

+
#> Time difference of 36.146 secs

 
R session information.

 
#> ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
 #>  setting  value
diff --git a/articles/spatialLIBD.html b/articles/spatialLIBD.html
index 1cc55604..2e7882be 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)
-#> 2024-07-19 16:14:32.734251 loading file /github/home/.cache/R/BiocFileCache/29a3cc87240_sce_sub_for_vignette.Rdata%3Fdl%3D1
+#> 2024-07-19 16:15:53.21679 loading file /github/home/.cache/R/BiocFileCache/29976b923e3_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)
-#> 2024-07-19 16:14:37.037444 loading file /github/home/.cache/R/BiocFileCache/29a67699111_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-07-19 16:15:57.68007 loading file /github/home/.cache/R/BiocFileCache/2993b875f9c_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
 modeling_results <- fetch_data("modeling_results", eh = ehub)
-#> 2024-07-19 16:14:37.470295 loading file /github/home/.cache/R/BiocFileCache/29a6df9f139_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1

+#> 2024-07-19 16:15:58.118208 loading file /github/home/.cache/R/BiocFileCache/2993f4cc32e_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 
-#>   9.878   0.312  10.191
+#>   9.899   0.292  10.210
 
 ## Explore the result
 class(sig_genes)
@@ -1377,9 +1377,9 @@ 
Reproducibilitylibrary("knitr")
 knit("spatialLIBD.Rmd", tangle = TRUE)

 
Date the vignette was generated.

-
#> [1] "2024-07-19 16:14:54 UTC"

+
#> [1] "2024-07-19 16:16:15 UTC"

 
Wallclock time spent generating the vignette.

-
#> Time difference of 34.825 secs

+
#> Time difference of 35.069 secs

 
R session information.

 
#> ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
 #>  setting  value
diff --git a/pkgdown.yml b/pkgdown.yml
index 98ccbc45..666d2294 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: 2024-07-19T16:07Z
+last_built: 2024-07-19T16:08Z
diff --git a/reference/add_images.html b/reference/add_images.html
index 4e9a1e4b..bcba8845 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")
     ))
 }
-#> 2024-07-19 16:07:22.408291 loading file /github/home/.cache/R/BiocFileCache/d682f29a8c2_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
-#> 2024-07-19 16:07:37.850974 adding image for sample 151507
-#> 2024-07-19 16:07:38.796288 adding image for sample 151508
+#> 2024-07-19 16:08:46.987633 loading file /github/home/.cache/R/BiocFileCache/d677ad96a3a_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-07-19 16:09:02.236729 adding image for sample 151507
+#> 2024-07-19 16:09:03.039824 adding image for sample 151508
 #> Warning: No image was found for sample: 151508
-#> 2024-07-19 16:07:38.796601 adding image for sample 151509
+#> 2024-07-19 16:09:03.040133 adding image for sample 151509
 #> Warning: No image was found for sample: 151509
-#> 2024-07-19 16:07:38.796806 adding image for sample 151510
+#> 2024-07-19 16:09:03.04034 adding image for sample 151510
 #> Warning: No image was found for sample: 151510
-#> 2024-07-19 16:07:38.797002 adding image for sample 151669
+#> 2024-07-19 16:09:03.040534 adding image for sample 151669
 #> Warning: No image was found for sample: 151669
-#> 2024-07-19 16:07:38.797189 adding image for sample 151670
+#> 2024-07-19 16:09:03.040724 adding image for sample 151670
 #> Warning: No image was found for sample: 151670
-#> 2024-07-19 16:07:38.797374 adding image for sample 151671
+#> 2024-07-19 16:09:03.040911 adding image for sample 151671
 #> Warning: No image was found for sample: 151671
-#> 2024-07-19 16:07:38.797563 adding image for sample 151672
+#> 2024-07-19 16:09:03.041105 adding image for sample 151672
 #> Warning: No image was found for sample: 151672
-#> 2024-07-19 16:07:38.79775 adding image for sample 151673
+#> 2024-07-19 16:09:03.041298 adding image for sample 151673
 #> Warning: No image was found for sample: 151673
-#> 2024-07-19 16:07:38.79797 adding image for sample 151674
+#> 2024-07-19 16:09:03.041488 adding image for sample 151674
 #> Warning: No image was found for sample: 151674
-#> 2024-07-19 16:07:38.798164 adding image for sample 151675
+#> 2024-07-19 16:09:03.041677 adding image for sample 151675
 #> Warning: No image was found for sample: 151675
-#> 2024-07-19 16:07:38.798351 adding image for sample 151676
+#> 2024-07-19 16:09:03.041864 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 c7e74049..2f7e7556 100644
--- a/reference/add_key.html
+++ b/reference/add_key.html
@@ -124,7 +124,7 @@ 
Examples

     spe$key_original <- NULL
     head(spe$key)
 }
-#> 2024-07-19 16:07:41.143035 loading file /github/home/.cache/R/BiocFileCache/d682f29a8c2_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-07-19 16:09:05.377842 loading file /github/home/.cache/R/BiocFileCache/d677ad96a3a_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 3e0f9ef6..8f5f0637 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")
-#> 2024-07-19 16:07:56.700429 loading file /github/home/.cache/R/BiocFileCache/29a5701c74f_spatialDLPFC_spe_subset_example.rds%3Fdl%3D1
+#> 2024-07-19 16:09:20.766803 loading file /github/home/.cache/R/BiocFileCache/29930f8862b_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 cd1c3b07..5b7d7d17 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")
 }
-#> 2024-07-19 16:08:09.317171 loading file /github/home/.cache/R/BiocFileCache/29a6df9f139_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
+#> 2024-07-19 16:09:33.269898 loading file /github/home/.cache/R/BiocFileCache/2993f4cc32e_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 5d36428f..646ef3dd 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")
 }
-#> 2024-07-19 16:08:10.288301 loading file /github/home/.cache/R/BiocFileCache/29a6df9f139_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
+#> 2024-07-19 16:09:34.327577 loading file /github/home/.cache/R/BiocFileCache/2993f4cc32e_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 b0055e79..bf011990 100644
--- a/reference/check_sce.html
+++ b/reference/check_sce.html
@@ -131,7 +131,7 @@ 
Examples

     ## Check the object
     check_sce(sce_example)
 }
-#> 2024-07-19 16:08:11.376681 loading file /github/home/.cache/R/BiocFileCache/29a3cc87240_sce_sub_for_vignette.Rdata%3Fdl%3D1
+#> 2024-07-19 16:09:35.314165 loading file /github/home/.cache/R/BiocFileCache/29976b923e3_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 41c7805d..eb08c811 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")
-#> 2024-07-19 16:08:13.754237 loading file /github/home/.cache/R/BiocFileCache/29a67699111_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-07-19 16:09:37.594883 loading file /github/home/.cache/R/BiocFileCache/2993b875f9c_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 a65976cf..db22d980 100644
--- a/reference/check_spe.html
+++ b/reference/check_spe.html
@@ -123,7 +123,7 @@ 
Examples

     ## Check the object
     check_spe(spe)
 }
-#> 2024-07-19 16:08:14.945897 loading file /github/home/.cache/R/BiocFileCache/d682f29a8c2_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-07-19 16:09:38.688891 loading file /github/home/.cache/R/BiocFileCache/d677ad96a3a_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 3c1b770f..6f2e85a6 100644
--- a/reference/cluster_export.html
+++ b/reference/cluster_export.html
@@ -134,7 +134,7 @@ 
Examples

     cluster_export(spe, "spatialLIBD")
     cluster_export(spe, "GraphBased")
 }
-#> 2024-07-19 16:08:29.580672 loading file /github/home/.cache/R/BiocFileCache/d682f29a8c2_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-07-19 16:09:53.217849 loading file /github/home/.cache/R/BiocFileCache/d677ad96a3a_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 e7ddd272..f5ce0db7 100644
--- a/reference/cluster_import.html
+++ b/reference/cluster_import.html
@@ -137,11 +137,11 @@ 
Examples

     ## Re-import them
     colData(cluster_import(spe))
 }
-#> 2024-07-19 16:08:44.680653 loading file /github/home/.cache/R/BiocFileCache/d682f29a8c2_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-07-19 16:10:08.30569 loading file /github/home/.cache/R/BiocFileCache/d677ad96a3a_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
 #> Overwriting 'spe$key'. Set 'overwrite = FALSE' if you do not want to overwrite it.
-#> Warning: '/tmp/Rtmpa9DJI7/exported_clusters/spatialLIBD' already exists
+#> Warning: '/tmp/Rtmp7S76vH/exported_clusters/spatialLIBD' already exists
 #> Overwriting 'spe$key'. Set 'overwrite = FALSE' if you do not want to overwrite it.
-#> Warning: '/tmp/Rtmpa9DJI7/exported_clusters/GraphBased' already exists
+#> Warning: '/tmp/Rtmp7S76vH/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 63fdac77..420b645f 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")
-#> 2024-07-19 16:09:00.041345 loading file /github/home/.cache/R/BiocFileCache/29a67699111_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-07-19 16:10:23.539115 loading file /github/home/.cache/R/BiocFileCache/2993b875f9c_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 c4dbcacf..01b09bdb 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")
 }
-#> 2024-07-19 16:09:02.518133 loading file /github/home/.cache/R/BiocFileCache/d682f29a8c2_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-07-19 16:10:25.973969 loading file /github/home/.cache/R/BiocFileCache/d677ad96a3a_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 fd0d8562..ebb0d2f8 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")
 }
-#> 2024-07-19 16:09:16.635003 loading file /github/home/.cache/R/BiocFileCache/29a6df9f139_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
+#> 2024-07-19 16:10:39.848614 loading file /github/home/.cache/R/BiocFileCache/2993f4cc32e_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 a6d0ff3e..1921a5e6 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")
 }
-#> 2024-07-19 16:09:17.847532 loading file /github/home/.cache/R/BiocFileCache/29a6df9f139_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
+#> 2024-07-19 16:10:41.046738 loading file /github/home/.cache/R/BiocFileCache/2993f4cc32e_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 6485f4fd..2eaf37a8 100644
--- a/reference/geom_spatial.html
+++ b/reference/geom_spatial.html
@@ -175,7 +175,7 @@ 
Examples

     ## Clean up
     rm(spe_sub)
 }
-#> 2024-07-19 16:09:19.772387 loading file /github/home/.cache/R/BiocFileCache/d682f29a8c2_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-07-19 16:10:42.748203 loading file /github/home/.cache/R/BiocFileCache/d677ad96a3a_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
 
 

     
diff --git a/reference/get_colors.html b/reference/get_colors.html
index 5ee0eaee..d5cf2bea 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")
-#> 2024-07-19 16:09:35.050203 loading file /github/home/.cache/R/BiocFileCache/29a67699111_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-07-19 16:10:58.0516 loading file /github/home/.cache/R/BiocFileCache/2993b875f9c_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 b098b04e..b5f0259c 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)
 }
-#> 2024-07-19 16:09:36.264848 loading file /github/home/.cache/R/BiocFileCache/d682f29a8c2_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-07-19 16:10:59.249658 loading file /github/home/.cache/R/BiocFileCache/d677ad96a3a_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
 
 

     
diff --git a/reference/img_update.html b/reference/img_update.html
index b091564c..ee1e666f 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))
 }
-#> 2024-07-19 16:09:51.600009 loading file /github/home/.cache/R/BiocFileCache/d682f29a8c2_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-07-19 16:11:15.049105 loading file /github/home/.cache/R/BiocFileCache/d677ad96a3a_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 d55bdfd5..c942f827 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))
 }
-#> 2024-07-19 16:10:05.774857 loading file /github/home/.cache/R/BiocFileCache/d682f29a8c2_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-07-19 16:11:29.065081 loading file /github/home/.cache/R/BiocFileCache/d677ad96a3a_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 9486e30f..6e012eb3 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")
 }
-#> 2024-07-19 16:10:22.541804 loading file /github/home/.cache/R/BiocFileCache/29a6df9f139_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
+#> 2024-07-19 16:11:45.58993 loading file /github/home/.cache/R/BiocFileCache/2993f4cc32e_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
 if (!exists("sce_layer")) sce_layer <- fetch_data(type = "sce_layer")
-#> 2024-07-19 16:10:23.419768 loading file /github/home/.cache/R/BiocFileCache/29a67699111_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-07-19 16:11:46.462236 loading file /github/home/.cache/R/BiocFileCache/2993b875f9c_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 4b24508b..c23b9085 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")
 }
-#> 2024-07-19 16:10:26.827106 loading file /github/home/.cache/R/BiocFileCache/29a6df9f139_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
+#> 2024-07-19 16:11:49.673814 loading file /github/home/.cache/R/BiocFileCache/2993f4cc32e_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 c4838e45..5a528ed7 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")
 }
-#> 2024-07-19 16:10:27.932675 loading file /github/home/.cache/R/BiocFileCache/29a6df9f139_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
+#> 2024-07-19 16:11:50.769974 loading file /github/home/.cache/R/BiocFileCache/2993f4cc32e_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 57498a84..6c8d871a 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)
-#> 2024-07-19 16:10:31.154749 make pseudobulk object
-#> 2024-07-19 16:10:31.333972 drop lowly expressed genes
-#> 2024-07-19 16:10:31.402817 normalize expression
+#> 2024-07-19 16:11:53.889601 make pseudobulk object
+#> 2024-07-19 16:11:54.064085 drop lowly expressed genes
+#> 2024-07-19 16:11:54.130567 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")
-#> 2024-07-19 16:10:31.480569 create model matrix
+#> 2024-07-19 16:11:54.20564 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)
-#> 2024-07-19 16:10:31.493248 run duplicateCorrelation()
-#> 2024-07-19 16:10:32.781093 The estimated correlation is: -0.0187869166526901
+#> 2024-07-19 16:11:54.217661 run duplicateCorrelation()
+#> 2024-07-19 16:11:55.455792 The estimated correlation is: -0.0187869166526901
diff --git a/reference/registration_model.html b/reference/registration_model.html index b466b60b..02fb5a38 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) -#> 2024-07-19 16:10:33.217748 make pseudobulk object -#> 2024-07-19 16:10:33.403467 drop lowly expressed genes -#> 2024-07-19 16:10:33.458532 normalize expression +#> 2024-07-19 16:11:55.899633 make pseudobulk object +#> 2024-07-19 16:11:56.080251 drop lowly expressed genes +#> 2024-07-19 16:11:56.132492 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") -#> 2024-07-19 16:10:33.532935 create model matrix +#> 2024-07-19 16:11:56.204297 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 1bf72d57..300aadf7 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) -#> 2024-07-19 16:10:33.990008 make pseudobulk object -#> 2024-07-19 16:10:34.145319 drop lowly expressed genes -#> 2024-07-19 16:10:34.199291 normalize expression +#> 2024-07-19 16:11:56.644418 make pseudobulk object +#> 2024-07-19 16:11:56.791668 drop lowly expressed genes +#> 2024-07-19 16:11:56.842951 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 b334c950..097e75b4 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) -#> 2024-07-19 16:10:34.787064 make pseudobulk object -#> 2024-07-19 16:10:34.965636 drop lowly expressed genes -#> 2024-07-19 16:10:35.019663 normalize expression +#> 2024-07-19 16:11:57.413559 make pseudobulk object +#> 2024-07-19 16:11:57.585532 drop lowly expressed genes +#> 2024-07-19 16:11:57.637466 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") -#> 2024-07-19 16:10:35.092247 create model matrix +#> 2024-07-19 16:11:57.709037 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) -#> 2024-07-19 16:10:35.104275 run duplicateCorrelation() -#> 2024-07-19 16:10:36.383178 The estimated correlation is: -0.0187869166526901 +#> 2024-07-19 16:11:57.719706 run duplicateCorrelation() +#> 2024-07-19 16:11:58.954803 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" ) -#> 2024-07-19 16:10:36.395592 computing F-statistics +#> 2024-07-19 16:11:58.966842 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" ) -#> 2024-07-19 16:10:36.457284 computing F-statistics +#> 2024-07-19 16:11:59.027537 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" ) -#> 2024-07-19 16:10:36.506898 computing F-statistics +#> 2024-07-19 16:11:59.076113 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 cd23b136..0a906ac7 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) -#> 2024-07-19 16:10:37.070904 make pseudobulk object -#> 2024-07-19 16:10:37.224566 drop lowly expressed genes -#> 2024-07-19 16:10:37.278291 normalize expression +#> 2024-07-19 16:11:59.626354 make pseudobulk object +#> 2024-07-19 16:11:59.774447 drop lowly expressed genes +#> 2024-07-19 16:11:59.826491 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") -#> 2024-07-19 16:10:37.35073 create model matrix +#> 2024-07-19 16:11:59.897296 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) -#> 2024-07-19 16:10:37.36194 run duplicateCorrelation() -#> 2024-07-19 16:10:38.660422 The estimated correlation is: -0.0187869166526901 +#> 2024-07-19 16:11:59.908064 run duplicateCorrelation() +#> 2024-07-19 16:12:01.17622 The estimated correlation is: -0.0187869166526901 results_enrichment <- registration_stats_enrichment(sce_pseudo, block_cor, "age", gene_ensembl = "ensembl", gene_name = "gene_name" ) -#> 2024-07-19 16:10:38.664043 computing enrichment statistics -#> 2024-07-19 16:10:38.780433 extract and reformat enrichment results +#> 2024-07-19 16:12:01.179778 computing enrichment statistics +#> 2024-07-19 16:12:01.293937 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" ) -#> 2024-07-19 16:10:38.812893 computing enrichment statistics -#> 2024-07-19 16:10:38.915076 extract and reformat enrichment results +#> 2024-07-19 16:12:01.32589 computing enrichment statistics +#> 2024-07-19 16:12:01.426231 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 916013c2..93e9e78b 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) -#> 2024-07-19 16:10:39.376626 make pseudobulk object -#> 2024-07-19 16:10:39.529488 drop lowly expressed genes -#> 2024-07-19 16:10:39.583602 normalize expression +#> 2024-07-19 16:12:01.87913 make pseudobulk object +#> 2024-07-19 16:12:02.028845 drop lowly expressed genes +#> 2024-07-19 16:12:02.081427 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") -#> 2024-07-19 16:10:39.682072 create model matrix +#> 2024-07-19 16:12:02.179267 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) -#> 2024-07-19 16:10:39.693149 run duplicateCorrelation() -#> 2024-07-19 16:10:40.967476 The estimated correlation is: -0.0187869166526901 +#> 2024-07-19 16:12:02.189909 run duplicateCorrelation() +#> 2024-07-19 16:12:03.421199 The estimated correlation is: -0.0187869166526901 results_pairwise <- registration_stats_pairwise(sce_pseudo, registration_mod, block_cor, gene_ensembl = "ensembl", gene_name = "gene_name" ) -#> 2024-07-19 16:10:40.969445 running the baseline pairwise model -#> 2024-07-19 16:10:40.985843 computing pairwise statistics +#> 2024-07-19 16:12:03.423083 running the baseline pairwise model +#> 2024-07-19 16:12:03.439296 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" ) -#> 2024-07-19 16:10:41.050011 running the baseline pairwise model -#> 2024-07-19 16:10:41.067112 computing pairwise statistics +#> 2024-07-19 16:12:03.503117 running the baseline pairwise model +#> 2024-07-19 16:12:03.520061 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 800bb058..aaf69a89 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" ) -#> 2024-07-19 16:10:41.620107 make pseudobulk object -#> 2024-07-19 16:10:41.774995 dropping 9 pseudo-bulked samples that are below 'min_ncells'. -#> 2024-07-19 16:10:41.796912 drop lowly expressed genes -#> 2024-07-19 16:10:41.852361 normalize expression -#> 2024-07-19 16:10:41.910191 create model matrix -#> 2024-07-19 16:10:41.92079 run duplicateCorrelation() -#> 2024-07-19 16:10:44.324436 The estimated correlation is: -0.0783081238514532 -#> 2024-07-19 16:10:44.326643 computing enrichment statistics -#> 2024-07-19 16:10:44.442721 extract and reformat enrichment results -#> 2024-07-19 16:10:44.468326 running the baseline pairwise model -#> 2024-07-19 16:10:44.486197 computing pairwise statistics -#> 2024-07-19 16:10:44.560061 computing F-statistics +#> 2024-07-19 16:12:04.057719 make pseudobulk object +#> 2024-07-19 16:12:04.203799 dropping 9 pseudo-bulked samples that are below 'min_ncells'. +#> 2024-07-19 16:12:04.223933 drop lowly expressed genes +#> 2024-07-19 16:12:04.27522 normalize expression +#> 2024-07-19 16:12:04.329804 create model matrix +#> 2024-07-19 16:12:04.339691 run duplicateCorrelation() +#> 2024-07-19 16:12:06.691905 The estimated correlation is: -0.0783081238514532 +#> 2024-07-19 16:12:06.694049 computing enrichment statistics +#> 2024-07-19 16:12:06.806364 extract and reformat enrichment results +#> 2024-07-19 16:12:06.831469 running the baseline pairwise model +#> 2024-07-19 16:12:06.853505 computing pairwise statistics +#> 2024-07-19 16:12:06.927273 computing F-statistics diff --git a/reference/sce_to_spe.html b/reference/sce_to_spe.html index e1b882a6..20d44a06 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) } -#> 2024-07-19 16:10:46.443173 loading file /github/home/.cache/R/BiocFileCache/d682f29a8c2_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-07-19 16:12:08.737406 loading file /github/home/.cache/R/BiocFileCache/d677ad96a3a_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 972ca003..f0ac6e31 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") } -#> 2024-07-19 16:10:59.439626 loading file /github/home/.cache/R/BiocFileCache/29a6df9f139_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1 +#> 2024-07-19 16:12:21.946697 loading file /github/home/.cache/R/BiocFileCache/2993f4cc32e_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1 if (!exists("sce_layer")) sce_layer <- fetch_data(type = "sce_layer") -#> 2024-07-19 16:11:00.380846 loading file /github/home/.cache/R/BiocFileCache/29a67699111_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-07-19 16:12:22.866015 loading file /github/home/.cache/R/BiocFileCache/2993b875f9c_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 c3b5c867..da27511d 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") } -#> 2024-07-19 16:11:04.11671 loading file /github/home/.cache/R/BiocFileCache/29a6df9f139_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1 +#> 2024-07-19 16:12:26.492838 loading file /github/home/.cache/R/BiocFileCache/2993f4cc32e_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1 if (!exists("sce_layer")) sce_layer <- fetch_data(type = "sce_layer") -#> 2024-07-19 16:11:05.078106 loading file /github/home/.cache/R/BiocFileCache/29a67699111_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-07-19 16:12:27.448996 loading file /github/home/.cache/R/BiocFileCache/2993b875f9c_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 93edef26..cb4e8ccc 100644 --- a/reference/vis_clus.html +++ b/reference/vis_clus.html @@ -242,7 +242,7 @@

Examples

) print(p4) } -#> 2024-07-19 16:11:07.56844 loading file /github/home/.cache/R/BiocFileCache/d682f29a8c2_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-07-19 16:12:29.789018 loading file /github/home/.cache/R/BiocFileCache/d677ad96a3a_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 f7a53154..1c4a4104 100644 --- a/reference/vis_clus_p.html +++ b/reference/vis_clus_p.html @@ -202,7 +202,7 @@

Examples

## Clean up rm(spe_sub) } -#> 2024-07-19 16:11:26.792648 loading file /github/home/.cache/R/BiocFileCache/d682f29a8c2_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-07-19 16:12:48.654148 loading file /github/home/.cache/R/BiocFileCache/d677ad96a3a_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 diff --git a/reference/vis_gene.html b/reference/vis_gene.html index 0af066ac..225351d8 100644 --- a/reference/vis_gene.html +++ b/reference/vis_gene.html @@ -341,7 +341,7 @@

Examples

) print(p8) } -#> 2024-07-19 16:11:41.686731 loading file /github/home/.cache/R/BiocFileCache/d682f29a8c2_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-07-19 16:13:03.274048 loading file /github/home/.cache/R/BiocFileCache/d677ad96a3a_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 b54dba4c..28bb6d92 100644 --- a/reference/vis_gene_p.html +++ b/reference/vis_gene_p.html @@ -215,7 +215,7 @@

Examples

## Clean up rm(spe_sub) } -#> 2024-07-19 16:12:07.80877 loading file /github/home/.cache/R/BiocFileCache/d682f29a8c2_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-07-19 16:13:28.907896 loading file /github/home/.cache/R/BiocFileCache/d677ad96a3a_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 8070a36e..147ec364 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) } -#> 2024-07-19 16:12:22.629178 loading file /github/home/.cache/R/BiocFileCache/d682f29a8c2_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-07-19 16:13:43.592169 loading file /github/home/.cache/R/BiocFileCache/d677ad96a3a_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 01a73127..14e89641 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) } -#> 2024-07-19 16:12:38.901329 loading file /github/home/.cache/R/BiocFileCache/d682f29a8c2_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-07-19 16:13:59.908226 loading file /github/home/.cache/R/BiocFileCache/d677ad96a3a_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1