diff --git a/articles/TenX_data_download.html b/articles/TenX_data_download.html index 562f5bb7..c759162c 100644 --- a/articles/TenX_data_download.html +++ b/articles/TenX_data_download.html @@ -535,7 +535,7 @@

From Gencode## Show the GTF cache location gtf_cache #> BFC4 -#> "/github/home/.cache/R/BiocFileCache/66d15d0acd6_gencode.v32.annotation.gtf.gz" +#> "/github/home/.cache/R/BiocFileCache/66d495fe6b5_gencode.v32.annotation.gtf.gz" ## Import into R (takes ~1 min) gtf <- rtracklayer::import(gtf_cache) @@ -821,11 +821,11 @@

Wrapper functions= c("lowres", "hires", "detected", "aligned"), load = TRUE, reference_gtf = gtf_cache ) -#> 2024-03-28 14:40:40.654767 SpatialExperiment::read10xVisium: reading basic data from SpaceRanger -#> 2024-03-28 14:40:51.947897 read10xVisiumAnalysis: reading analysis output from SpaceRanger -#> 2024-03-28 14:40:52.979696 add10xVisiumAnalysis: adding analysis output from SpaceRanger -#> 2024-03-28 14:40:53.226671 rtracklayer::import: reading the reference GTF file -#> 2024-03-28 14:41:20.35758 adding gene information to the SPE object +#> 2024-03-28 18:09:16.041334 SpatialExperiment::read10xVisium: reading basic data from SpaceRanger +#> 2024-03-28 18:09:27.422562 read10xVisiumAnalysis: reading analysis output from SpaceRanger +#> 2024-03-28 18:09:28.513278 add10xVisiumAnalysis: adding analysis output from SpaceRanger +#> 2024-03-28 18:09:28.771913 rtracklayer::import: reading the reference GTF file +#> 2024-03-28 18:09:55.671206 adding gene information to the SPE object #> Warning: Gene IDs did not match. This typically happens when you are not using #> the same GTF file as the one that was used by SpaceRanger. For example, one #> file uses GENCODE IDs and the other one ENSEMBL IDs. read10xVisiumWrapper() @@ -833,7 +833,7 @@

Wrapper functions#> Warning: Dropping 29 out of 36601 genes for which we don't have information on #> the reference GTF file. This typically happens when you are not using the same #> GTF file as the one that was used by SpaceRanger. -#> 2024-03-28 14:41:21.891865 adding information used by spatialLIBD +#> 2024-03-28 18:09:57.229048 adding information used by spatialLIBD 
 ## Run our shiny app
 if (interactive()) {
@@ -1117,9 +1117,9 @@ 
Reproducibilitylibrary("knitr")
 knit("TenX_data_download.Rmd", tangle = TRUE)

Date the vignette was generated.

-
#> [1] "2024-03-28 14:41:23 UTC"
+
#> [1] "2024-03-28 18:09:58 UTC"

Wallclock time spent generating the vignette.

-
#> Time difference of 1.8 mins
+
#> Time difference of 1.815 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 8a33cd1a..93f946b6 100644
--- a/articles/guide_to_spatial_registration.html
+++ b/articles/guide_to_spatial_registration.html
@@ -287,7 +287,7 @@ 
Spatial Reference
 ## get reference layer enrichment statistics
 layer_modeling_results <- fetch_data(type = "modeling_results")
-#> 2024-03-28 14:41:43.237136 loading file /github/home/.cache/R/BiocFileCache/66d3eb2c813_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
+#> 2024-03-28 18:10:17.22308 loading file /github/home/.cache/R/BiocFileCache/66d27e2efcd_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
 
 layer_modeling_results$enrichment[1:5, 1:5]
 #>    t_stat_WM t_stat_Layer1 t_stat_Layer2 t_stat_Layer3 t_stat_Layer4
@@ -389,18 +389,18 @@ 
Get Enrichment statistics
     gene_ensembl = "gene_id",
     gene_name = "gene_name"
 )
-#> 2024-03-28 14:41:50.998656 make pseudobulk object
-#> 2024-03-28 14:41:52.668731 dropping 13 pseudo-bulked samples that are below 'min_ncells'.
-#> 2024-03-28 14:41:52.726515 drop lowly expressed genes
-#> 2024-03-28 14:41:52.906506 normalize expression
-#> 2024-03-28 14:41:54.375036 create model matrix
-#> 2024-03-28 14:41:54.399107 run duplicateCorrelation()
-#> 2024-03-28 14:42:07.720443 The estimated correlation is: 0.138734774807097
-#> 2024-03-28 14:42:07.722943 computing enrichment statistics
-#> 2024-03-28 14:42:08.787755 extract and reformat enrichment results
-#> 2024-03-28 14:42:08.840827 running the baseline pairwise model
-#> 2024-03-28 14:42:09.000495 computing pairwise statistics
-#> 2024-03-28 14:42:10.332619 computing F-statistics

+#> 2024-03-28 18:10:25.070578 make pseudobulk object
+#> 2024-03-28 18:10:26.783581 dropping 13 pseudo-bulked samples that are below 'min_ncells'.
+#> 2024-03-28 18:10:26.845477 drop lowly expressed genes
+#> 2024-03-28 18:10:27.031879 normalize expression
+#> 2024-03-28 18:10:28.549362 create model matrix
+#> 2024-03-28 18:10:28.574032 run duplicateCorrelation()
+#> 2024-03-28 18:10:42.456294 The estimated correlation is: 0.138734774807097
+#> 2024-03-28 18:10:42.459062 computing enrichment statistics
+#> 2024-03-28 18:10:43.549087 extract and reformat enrichment results
+#> 2024-03-28 18:10:43.603743 running the baseline pairwise model
+#> 2024-03-28 18:10:43.762835 computing pairwise statistics
+#> 2024-03-28 18:10:45.105492 computing F-statistics

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

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

Date the vignette was generated.

-
#> [1] "2024-03-28 14:42:11 UTC"
+
#> [1] "2024-03-28 18:10:46 UTC"

Wallclock time spent generating the vignette.

-
#> Time difference of 41.749 secs
+
#> Time difference of 42.307 secs

R session information.

#> ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
 #>  setting  value
diff --git a/articles/multi_gene_plots.html b/articles/multi_gene_plots.html
index 08db155a..01a5e0d2 100644
--- a/articles/multi_gene_plots.html
+++ b/articles/multi_gene_plots.html
@@ -197,9 +197,9 @@ 
Plotting One Gene
 modeling_results <- fetch_data(type = "modeling_results")
-#> 2024-03-28 14:42:36.745484 loading file /github/home/.cache/R/BiocFileCache/66d3eb2c813_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
+#> 2024-03-28 18:11:10.729518 loading file /github/home/.cache/R/BiocFileCache/66d27e2efcd_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
 sce_layer <- fetch_data(type = "sce_layer")
-#> 2024-03-28 14:42:37.980378 loading file /github/home/.cache/R/BiocFileCache/66d3004a813_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-03-28 18:11:11.556282 loading file /github/home/.cache/R/BiocFileCache/66d3007816b_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
 sig_genes <- sig_genes_extract_all(
     n = 400,
     modeling_results = modeling_results,
@@ -423,9 +423,9 @@ 
Reproducibilitylibrary("knitr")
 knit("multi_gene_plots.Rmd", tangle = TRUE)

 
Date the vignette was generated.

-
#> [1] "2024-03-28 14:42:54 UTC"

+
#> [1] "2024-03-28 18:11:28 UTC"

 
Wallclock time spent generating the vignette.

-
#> Time difference of 39.421 secs

+
#> Time difference of 38.32 secs

 
R session information.

 
#> ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
 #>  setting  value
diff --git a/articles/spatialLIBD.html b/articles/spatialLIBD.html
index 0c2c6cea..123950ff 100644
--- a/articles/spatialLIBD.html
+++ b/articles/spatialLIBD.html
@@ -417,7 +417,7 @@ 
Downloading the data with s
 
 ## Download the small example sce data
 sce <- fetch_data(type = "sce_example", eh = ehub)
-#> 2024-03-28 14:43:11.892682 loading file /github/home/.cache/R/BiocFileCache/66d35080796_sce_sub_for_vignette.Rdata%3Fdl%3D1
+#> 2024-03-28 18:11:45.303478 loading file /github/home/.cache/R/BiocFileCache/66d4c2bf328_sce_sub_for_vignette.Rdata%3Fdl%3D1
 
 ## Convert to a SpatialExperiment object
 spe <- sce_to_spe(sce)
@@ -429,9 +429,9 @@ 
Downloading the data with s
 
 ## Query ExperimentHub and download the data
 if (!exists("sce_layer")) sce_layer <- fetch_data(type = "sce_layer", eh = ehub)
-#> 2024-03-28 14:43:17.909918 loading file /github/home/.cache/R/BiocFileCache/66d3004a813_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-03-28 18:11:49.994273 loading file /github/home/.cache/R/BiocFileCache/66d3007816b_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
 modeling_results <- fetch_data("modeling_results", eh = ehub)
-#> 2024-03-28 14:43:18.361514 loading file /github/home/.cache/R/BiocFileCache/66d3eb2c813_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1

+#> 2024-03-28 18:11:50.475533 loading file /github/home/.cache/R/BiocFileCache/66d27e2efcd_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1

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

 
@@ -504,7 +504,7 @@ 
Downloading the data with s
         )
 )
 #>    user  system elapsed 
-#>  10.188   0.444  10.674
+#>  10.502   0.388  10.930
 
 ## Explore the result
 class(sig_genes)
@@ -1380,9 +1380,9 @@ 
Reproducibilitylibrary("knitr")
 knit("spatialLIBD.Rmd", tangle = TRUE)

 
Date the vignette was generated.

-
#> [1] "2024-03-28 14:43:36 UTC"

+
#> [1] "2024-03-28 18:12:08 UTC"

 
Wallclock time spent generating the vignette.

-
#> Time difference of 38.479 secs

+
#> Time difference of 37.334 secs

 
R session information.

 
#> ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
 #>  setting  value
diff --git a/pkgdown.yml b/pkgdown.yml
index 0299eb39..cbde3053 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -6,5 +6,5 @@ articles:
   guide_to_spatial_registration: guide_to_spatial_registration.html
   multi_gene_plots: multi_gene_plots.html
   spatialLIBD: spatialLIBD.html
-last_built: 2024-03-28T14:33Z
+last_built: 2024-03-28T18:02Z
 
diff --git a/reference/add_images.html b/reference/add_images.html
index d8254bbc..b3ee8dc2 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")
     ))
 }
-#> 2024-03-28 14:33:56.244096 loading file /github/home/.cache/R/BiocFileCache/a7114b37d42_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
-#> 2024-03-28 14:34:12.160331 adding image for sample 151507
-#> 2024-03-28 14:34:13.904375 adding image for sample 151508
+#> 2024-03-28 18:02:50.931828 loading file /github/home/.cache/R/BiocFileCache/a7153961056_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-03-28 18:03:06.724324 adding image for sample 151507
+#> 2024-03-28 18:03:07.450262 adding image for sample 151508
 #> Warning: No image was found for sample: 151508
-#> 2024-03-28 14:34:13.904688 adding image for sample 151509
+#> 2024-03-28 18:03:07.450615 adding image for sample 151509
 #> Warning: No image was found for sample: 151509
-#> 2024-03-28 14:34:13.904895 adding image for sample 151510
+#> 2024-03-28 18:03:07.450829 adding image for sample 151510
 #> Warning: No image was found for sample: 151510
-#> 2024-03-28 14:34:13.905096 adding image for sample 151669
+#> 2024-03-28 18:03:07.451035 adding image for sample 151669
 #> Warning: No image was found for sample: 151669
-#> 2024-03-28 14:34:13.905289 adding image for sample 151670
+#> 2024-03-28 18:03:07.451233 adding image for sample 151670
 #> Warning: No image was found for sample: 151670
-#> 2024-03-28 14:34:13.90548 adding image for sample 151671
+#> 2024-03-28 18:03:07.451429 adding image for sample 151671
 #> Warning: No image was found for sample: 151671
-#> 2024-03-28 14:34:13.905672 adding image for sample 151672
+#> 2024-03-28 18:03:07.451623 adding image for sample 151672
 #> Warning: No image was found for sample: 151672
-#> 2024-03-28 14:34:13.905859 adding image for sample 151673
+#> 2024-03-28 18:03:07.451815 adding image for sample 151673
 #> Warning: No image was found for sample: 151673
-#> 2024-03-28 14:34:13.906047 adding image for sample 151674
+#> 2024-03-28 18:03:07.452006 adding image for sample 151674
 #> Warning: No image was found for sample: 151674
-#> 2024-03-28 14:34:13.906235 adding image for sample 151675
+#> 2024-03-28 18:03:07.452202 adding image for sample 151675
 #> Warning: No image was found for sample: 151675
-#> 2024-03-28 14:34:13.906427 adding image for sample 151676
+#> 2024-03-28 18:03:07.452401 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 9977ca37..5af14c69 100644
--- a/reference/add_key.html
+++ b/reference/add_key.html
@@ -117,7 +117,7 @@ 
Examples

     ## Note that the original 'key' order was 'sample_id'_'barcode' and we'
     ## have since changed it to 'barcode'_'sample_id'.
 }
-#> 2024-03-28 14:34:16.523784 loading file /github/home/.cache/R/BiocFileCache/a7114b37d42_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-03-28 18:03:09.60679 loading file /github/home/.cache/R/BiocFileCache/a7153961056_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
 #> [1] "AAACAACGAATAGTTC-1_151507" "AAACAAGTATCTCCCA-1_151507"
 #> [3] "AAACAATCTACTAGCA-1_151507" "AAACACCAATAACTGC-1_151507"
 #> [5] "AAACAGCTTTCAGAAG-1_151507" "AAACAGGGTCTATATT-1_151507"
diff --git a/reference/annotate_registered_clusters.html b/reference/annotate_registered_clusters.html
index 00f96c85..38eb6513 100644
--- a/reference/annotate_registered_clusters.html
+++ b/reference/annotate_registered_clusters.html
@@ -139,7 +139,7 @@ 
Examples

 if (!exists("modeling_results")) {
     modeling_results <- fetch_data(type = "modeling_results")
 }
-#> 2024-03-28 14:34:31.633264 loading file /github/home/.cache/R/BiocFileCache/66d3eb2c813_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
+#> 2024-03-28 18:03:23.945122 loading file /github/home/.cache/R/BiocFileCache/66d27e2efcd_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 cbfed54b..2def6c8e 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")
 }
-#> 2024-03-28 14:34:32.96101 loading file /github/home/.cache/R/BiocFileCache/66d3eb2c813_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
+#> 2024-03-28 18:03:24.865109 loading file /github/home/.cache/R/BiocFileCache/66d27e2efcd_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 bb048d4e..8ac2071a 100644
--- a/reference/check_sce.html
+++ b/reference/check_sce.html
@@ -131,7 +131,7 @@ 
Examples

     ## Check the object
     check_sce(sce_example)
 }
-#> 2024-03-28 14:34:34.313455 loading file /github/home/.cache/R/BiocFileCache/66d35080796_sce_sub_for_vignette.Rdata%3Fdl%3D1
+#> 2024-03-28 18:03:25.805642 loading file /github/home/.cache/R/BiocFileCache/66d4c2bf328_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 7cd199d9..722e0051 100644
--- a/reference/check_sce_layer.html
+++ b/reference/check_sce_layer.html
@@ -111,7 +111,7 @@ 
Examples

     

 ## Obtain the necessary data
 if (!exists("sce_layer")) sce_layer <- fetch_data("sce_layer")
-#> 2024-03-28 14:34:37.137212 loading file /github/home/.cache/R/BiocFileCache/66d3004a813_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-03-28 18:03:28.265212 loading file /github/home/.cache/R/BiocFileCache/66d3007816b_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
 
 ## Check the object
 check_sce_layer(sce_layer)
diff --git a/reference/check_spe.html b/reference/check_spe.html
index 8a577edc..a56c11bd 100644
--- a/reference/check_spe.html
+++ b/reference/check_spe.html
@@ -123,7 +123,7 @@ 
Examples

     ## Check the object
     check_spe(spe)
 }
-#> 2024-03-28 14:34:39.430907 loading file /github/home/.cache/R/BiocFileCache/a7114b37d42_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-03-28 18:03:30.166875 loading file /github/home/.cache/R/BiocFileCache/a7153961056_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 30cbed11..1d5448fc 100644
--- a/reference/cluster_export.html
+++ b/reference/cluster_export.html
@@ -134,7 +134,7 @@ 
Examples

     cluster_export(spe, "spatialLIBD")
     cluster_export(spe, "GraphBased")
 }
-#> 2024-03-28 14:34:54.568023 loading file /github/home/.cache/R/BiocFileCache/a7114b37d42_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-03-28 18:03:44.653251 loading file /github/home/.cache/R/BiocFileCache/a7153961056_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 40f523c5..3e5ea7be 100644
--- a/reference/cluster_import.html
+++ b/reference/cluster_import.html
@@ -137,11 +137,11 @@ 
Examples

     ## Re-import them
     colData(cluster_import(spe))
 }
-#> 2024-03-28 14:35:09.550251 loading file /github/home/.cache/R/BiocFileCache/a7114b37d42_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-03-28 18:03:59.010386 loading file /github/home/.cache/R/BiocFileCache/a7153961056_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
 #> Overwriting 'spe$key'. Set 'overwrite = FALSE' if you do not want to overwrite it.
-#> Warning: '/tmp/RtmpZrib1s/exported_clusters/spatialLIBD' already exists
+#> Warning: '/tmp/RtmpRhLF2F/exported_clusters/spatialLIBD' already exists
 #> Overwriting 'spe$key'. Set 'overwrite = FALSE' if you do not want to overwrite it.
-#> Warning: '/tmp/RtmpZrib1s/exported_clusters/GraphBased' already exists
+#> Warning: '/tmp/RtmpRhLF2F/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 e678f820..9bc461cd 100644
--- a/reference/fetch_data.html
+++ b/reference/fetch_data.html
@@ -165,7 +165,7 @@ 
Examples

 ## Download the SingleCellExperiment object
 ## at the layer-level
 if (!exists("sce_layer")) sce_layer <- fetch_data("sce_layer")
-#> 2024-03-28 14:35:25.736324 loading file /github/home/.cache/R/BiocFileCache/66d3004a813_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-03-28 18:04:14.395956 loading file /github/home/.cache/R/BiocFileCache/66d3007816b_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 a4287cc4..d2a5299d 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")
 }
-#> 2024-03-28 14:35:27.867714 loading file /github/home/.cache/R/BiocFileCache/a7114b37d42_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-03-28 18:04:16.022901 loading file /github/home/.cache/R/BiocFileCache/a7153961056_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 16c331ac..2f197334 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")
 }
-#> 2024-03-28 14:35:43.512626 loading file /github/home/.cache/R/BiocFileCache/66d3eb2c813_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
+#> 2024-03-28 18:04:30.900128 loading file /github/home/.cache/R/BiocFileCache/66d27e2efcd_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 86ded7ef..03884a38 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")
 }
-#> 2024-03-28 14:35:45.147352 loading file /github/home/.cache/R/BiocFileCache/66d3eb2c813_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
+#> 2024-03-28 18:04:32.144349 loading file /github/home/.cache/R/BiocFileCache/66d27e2efcd_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 683f0598..2b6a9436 100644
--- a/reference/geom_spatial.html
+++ b/reference/geom_spatial.html
@@ -175,7 +175,7 @@ 
Examples

     ## Clean up
     rm(spe_sub)
 }
-#> 2024-03-28 14:35:47.367253 loading file /github/home/.cache/R/BiocFileCache/a7114b37d42_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-03-28 18:04:34.044662 loading file /github/home/.cache/R/BiocFileCache/a7153961056_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
 
 

     
diff --git a/reference/get_colors.html b/reference/get_colors.html
index b0935232..f96c80dd 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")
-#> 2024-03-28 14:36:05.084936 loading file /github/home/.cache/R/BiocFileCache/66d3004a813_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-03-28 18:04:50.106049 loading file /github/home/.cache/R/BiocFileCache/66d3007816b_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 008bb820..80be9355 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)
 }
-#> 2024-03-28 14:36:06.589203 loading file /github/home/.cache/R/BiocFileCache/a7114b37d42_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-03-28 18:04:51.198996 loading file /github/home/.cache/R/BiocFileCache/a7153961056_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
 
 

     
diff --git a/reference/img_update.html b/reference/img_update.html
index 38e0c91e..9818042d 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))
 }
-#> 2024-03-28 14:36:22.930809 loading file /github/home/.cache/R/BiocFileCache/a7114b37d42_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-03-28 18:05:06.812165 loading file /github/home/.cache/R/BiocFileCache/a7153961056_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 0487bf34..035e959b 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))
 }
-#> 2024-03-28 14:36:37.711117 loading file /github/home/.cache/R/BiocFileCache/a7114b37d42_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-03-28 18:05:20.840242 loading file /github/home/.cache/R/BiocFileCache/a7153961056_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 7aa577fb..8e08696f 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")
 }
-#> 2024-03-28 14:36:55.056849 loading file /github/home/.cache/R/BiocFileCache/66d3eb2c813_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
+#> 2024-03-28 18:05:37.42147 loading file /github/home/.cache/R/BiocFileCache/66d27e2efcd_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
 if (!exists("sce_layer")) sce_layer <- fetch_data(type = "sce_layer")
-#> 2024-03-28 14:36:56.311122 loading file /github/home/.cache/R/BiocFileCache/66d3004a813_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-03-28 18:05:38.279673 loading file /github/home/.cache/R/BiocFileCache/66d3007816b_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 a2e0fa38..2ebffd0f 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")
 }
-#> 2024-03-28 14:37:00.302205 loading file /github/home/.cache/R/BiocFileCache/66d3eb2c813_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
+#> 2024-03-28 18:05:41.5575 loading file /github/home/.cache/R/BiocFileCache/66d27e2efcd_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 49e4a81f..b0b43b9e 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")
 }
-#> 2024-03-28 14:37:01.732162 loading file /github/home/.cache/R/BiocFileCache/66d3eb2c813_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
+#> 2024-03-28 18:05:42.589195 loading file /github/home/.cache/R/BiocFileCache/66d27e2efcd_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 fa173207..692bdd7e 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)
-#> 2024-03-28 14:37:03.753912 make pseudobulk object
-#> 2024-03-28 14:37:04.827185 drop lowly expressed genes
-#> 2024-03-28 14:37:04.89693 normalize expression
+#> 2024-03-28 18:05:44.654132 make pseudobulk object
+#> 2024-03-28 18:05:45.758217 drop lowly expressed genes
+#> 2024-03-28 18:05:45.830682 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")
-#> 2024-03-28 14:37:04.974511 create model matrix
+#> 2024-03-28 18:05:45.912232 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)
-#> 2024-03-28 14:37:04.987043 run duplicateCorrelation()
-#> 2024-03-28 14:37:06.282187 The estimated correlation is: -0.0187869166526901
+#> 2024-03-28 18:05:45.92567 run duplicateCorrelation()
+#> 2024-03-28 18:05:47.264243 The estimated correlation is: -0.0187869166526901
diff --git a/reference/registration_model.html b/reference/registration_model.html index fda7bdae..7cfabaf5 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) -#> 2024-03-28 14:37:06.695165 make pseudobulk object -#> 2024-03-28 14:37:06.909159 drop lowly expressed genes -#> 2024-03-28 14:37:06.962081 normalize expression +#> 2024-03-28 18:05:47.682867 make pseudobulk object +#> 2024-03-28 18:05:47.905607 drop lowly expressed genes +#> 2024-03-28 18:05:47.961348 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") -#> 2024-03-28 14:37:07.035333 create model matrix +#> 2024-03-28 18:05:48.038932 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 285e08b5..c39545a6 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) -#> 2024-03-28 14:37:07.445238 make pseudobulk object -#> 2024-03-28 14:37:07.600437 drop lowly expressed genes -#> 2024-03-28 14:37:07.653938 normalize expression +#> 2024-03-28 18:05:48.463877 make pseudobulk object +#> 2024-03-28 18:05:48.627844 drop lowly expressed genes +#> 2024-03-28 18:05:48.68396 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 fa638d0f..caae7b68 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) -#> 2024-03-28 14:37:08.267562 make pseudobulk object -#> 2024-03-28 14:37:08.42305 drop lowly expressed genes -#> 2024-03-28 14:37:08.477013 normalize expression +#> 2024-03-28 18:05:49.32449 make pseudobulk object +#> 2024-03-28 18:05:49.484694 drop lowly expressed genes +#> 2024-03-28 18:05:49.539838 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") -#> 2024-03-28 14:37:08.551488 create model matrix +#> 2024-03-28 18:05:49.615443 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) -#> 2024-03-28 14:37:08.562432 run duplicateCorrelation() -#> 2024-03-28 14:37:09.86522 The estimated correlation is: -0.0187869166526901 +#> 2024-03-28 18:05:49.626538 run duplicateCorrelation() +#> 2024-03-28 18:05:50.956394 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" ) -#> 2024-03-28 14:37:09.877329 computing F-statistics +#> 2024-03-28 18:05:50.968704 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" ) -#> 2024-03-28 14:37:09.940461 computing F-statistics +#> 2024-03-28 18:05:51.032693 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" ) -#> 2024-03-28 14:37:09.990436 computing F-statistics +#> 2024-03-28 18:05:51.085347 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 44caa44d..126ee35f 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) -#> 2024-03-28 14:37:10.555627 make pseudobulk object -#> 2024-03-28 14:37:10.71014 drop lowly expressed genes -#> 2024-03-28 14:37:10.764806 normalize expression +#> 2024-03-28 18:05:51.660948 make pseudobulk object +#> 2024-03-28 18:05:51.823014 drop lowly expressed genes +#> 2024-03-28 18:05:51.878513 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") -#> 2024-03-28 14:37:10.839214 create model matrix +#> 2024-03-28 18:05:51.95401 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) -#> 2024-03-28 14:37:10.850108 run duplicateCorrelation() -#> 2024-03-28 14:37:12.137778 The estimated correlation is: -0.0187869166526901 +#> 2024-03-28 18:05:51.965164 run duplicateCorrelation() +#> 2024-03-28 18:05:53.289559 The estimated correlation is: -0.0187869166526901 results_enrichment <- registration_stats_enrichment(sce_pseudo, block_cor, "age", gene_ensembl = "ensembl", gene_name = "gene_name" ) -#> 2024-03-28 14:37:12.141411 computing enrichment statistics -#> 2024-03-28 14:37:12.262002 extract and reformat enrichment results +#> 2024-03-28 18:05:53.293313 computing enrichment statistics +#> 2024-03-28 18:05:53.416483 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" ) -#> 2024-03-28 14:37:12.295261 computing enrichment statistics -#> 2024-03-28 14:37:12.399467 extract and reformat enrichment results +#> 2024-03-28 18:05:53.452327 computing enrichment statistics +#> 2024-03-28 18:05:53.558282 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 502863ff..7397b326 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) -#> 2024-03-28 14:37:12.880982 make pseudobulk object -#> 2024-03-28 14:37:13.034828 drop lowly expressed genes -#> 2024-03-28 14:37:13.088629 normalize expression +#> 2024-03-28 18:05:54.049647 make pseudobulk object +#> 2024-03-28 18:05:54.21604 drop lowly expressed genes +#> 2024-03-28 18:05:54.272032 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") -#> 2024-03-28 14:37:13.161665 create model matrix +#> 2024-03-28 18:05:54.349084 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) -#> 2024-03-28 14:37:13.172363 run duplicateCorrelation() -#> 2024-03-28 14:37:14.462183 The estimated correlation is: -0.0187869166526901 +#> 2024-03-28 18:05:54.3602 run duplicateCorrelation() +#> 2024-03-28 18:05:55.692137 The estimated correlation is: -0.0187869166526901 results_pairwise <- registration_stats_pairwise(sce_pseudo, registration_mod, block_cor, gene_ensembl = "ensembl", gene_name = "gene_name" ) -#> 2024-03-28 14:37:14.464154 running the baseline pairwise model -#> 2024-03-28 14:37:14.480677 computing pairwise statistics +#> 2024-03-28 18:05:55.694144 running the baseline pairwise model +#> 2024-03-28 18:05:55.71154 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" ) -#> 2024-03-28 14:37:14.547116 running the baseline pairwise model -#> 2024-03-28 14:37:14.564795 computing pairwise statistics +#> 2024-03-28 18:05:55.780169 running the baseline pairwise model +#> 2024-03-28 18:05:55.798245 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 17e26ac8..8d9ab801 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" ) -#> 2024-03-28 14:37:15.114537 make pseudobulk object -#> 2024-03-28 14:37:15.26948 dropping 9 pseudo-bulked samples that are below 'min_ncells'. -#> 2024-03-28 14:37:15.290824 drop lowly expressed genes -#> 2024-03-28 14:37:15.344636 normalize expression -#> 2024-03-28 14:37:15.402326 create model matrix -#> 2024-03-28 14:37:15.412564 run duplicateCorrelation() -#> 2024-03-28 14:37:17.791222 The estimated correlation is: -0.0783081238514532 -#> 2024-03-28 14:37:17.793365 computing enrichment statistics -#> 2024-03-28 14:37:17.943475 extract and reformat enrichment results -#> 2024-03-28 14:37:17.968483 running the baseline pairwise model -#> 2024-03-28 14:37:17.986351 computing pairwise statistics -#> 2024-03-28 14:37:18.059566 computing F-statistics +#> 2024-03-28 18:05:56.366935 make pseudobulk object +#> 2024-03-28 18:05:56.533999 dropping 9 pseudo-bulked samples that are below 'min_ncells'. +#> 2024-03-28 18:05:56.557996 drop lowly expressed genes +#> 2024-03-28 18:05:56.615048 normalize expression +#> 2024-03-28 18:05:56.674411 create model matrix +#> 2024-03-28 18:05:56.685387 run duplicateCorrelation() +#> 2024-03-28 18:05:59.171397 The estimated correlation is: -0.0783081238514532 +#> 2024-03-28 18:05:59.173753 computing enrichment statistics +#> 2024-03-28 18:05:59.333785 extract and reformat enrichment results +#> 2024-03-28 18:05:59.359841 running the baseline pairwise model +#> 2024-03-28 18:05:59.378139 computing pairwise statistics +#> 2024-03-28 18:05:59.453486 computing F-statistics diff --git a/reference/sce_to_spe.html b/reference/sce_to_spe.html index 704281ef..d31573ec 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) } -#> 2024-03-28 14:37:20.569812 loading file /github/home/.cache/R/BiocFileCache/a7114b37d42_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-03-28 18:06:01.316494 loading file /github/home/.cache/R/BiocFileCache/a7153961056_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 06d71813..a10c47a9 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") } -#> 2024-03-28 14:37:34.23598 loading file /github/home/.cache/R/BiocFileCache/66d3eb2c813_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1 +#> 2024-03-28 18:06:14.624236 loading file /github/home/.cache/R/BiocFileCache/66d27e2efcd_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1 if (!exists("sce_layer")) sce_layer <- fetch_data(type = "sce_layer") -#> 2024-03-28 14:37:35.391698 loading file /github/home/.cache/R/BiocFileCache/66d3004a813_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-03-28 18:06:15.391632 loading file /github/home/.cache/R/BiocFileCache/66d3007816b_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 f6683bbb..7d99ad06 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") } -#> 2024-03-28 14:37:39.524539 loading file /github/home/.cache/R/BiocFileCache/66d3eb2c813_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1 +#> 2024-03-28 18:06:19.210632 loading file /github/home/.cache/R/BiocFileCache/66d27e2efcd_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1 if (!exists("sce_layer")) sce_layer <- fetch_data(type = "sce_layer") -#> 2024-03-28 14:37:40.77721 loading file /github/home/.cache/R/BiocFileCache/66d3004a813_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-03-28 18:06:20.074073 loading file /github/home/.cache/R/BiocFileCache/66d3007816b_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 dc82d055..d76edbba 100644 --- a/reference/vis_clus.html +++ b/reference/vis_clus.html @@ -232,7 +232,7 @@

Examples

) print(p4) } -#> 2024-03-28 14:37:43.59266 loading file /github/home/.cache/R/BiocFileCache/a7114b37d42_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-03-28 18:06:22.291797 loading file /github/home/.cache/R/BiocFileCache/a7153961056_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 214acfbd..ce31a79e 100644 --- a/reference/vis_clus_p.html +++ b/reference/vis_clus_p.html @@ -202,7 +202,7 @@

Examples

## Clean up rm(spe_sub) } -#> 2024-03-28 14:38:03.953003 loading file /github/home/.cache/R/BiocFileCache/a7114b37d42_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-03-28 18:06:41.499933 loading file /github/home/.cache/R/BiocFileCache/a7153961056_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 diff --git a/reference/vis_gene.html b/reference/vis_gene.html index 83b80c29..f52d6cb6 100644 --- a/reference/vis_gene.html +++ b/reference/vis_gene.html @@ -331,7 +331,7 @@

Examples

) print(p8) } -#> 2024-03-28 14:38:19.548234 loading file /github/home/.cache/R/BiocFileCache/a7114b37d42_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-03-28 18:06:56.350183 loading file /github/home/.cache/R/BiocFileCache/a7153961056_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 0936a3bd..8e190381 100644 --- a/reference/vis_gene_p.html +++ b/reference/vis_gene_p.html @@ -220,7 +220,7 @@

Examples

## Clean up rm(spe_sub) } -#> 2024-03-28 14:38:46.322271 loading file /github/home/.cache/R/BiocFileCache/a7114b37d42_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-03-28 18:07:22.530345 loading file /github/home/.cache/R/BiocFileCache/a7153961056_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 b174ef75..18e7d578 100644 --- a/reference/vis_grid_clus.html +++ b/reference/vis_grid_clus.html @@ -227,7 +227,7 @@

Examples

## for subject 3 cowplot::plot_grid(plotlist = p_list, ncol = 2) } -#> 2024-03-28 14:39:02.156024 loading file /github/home/.cache/R/BiocFileCache/a7114b37d42_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-03-28 18:07:37.442968 loading file /github/home/.cache/R/BiocFileCache/a7153961056_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 85ec6fb0..80ee2a4e 100644 --- a/reference/vis_grid_gene.html +++ b/reference/vis_grid_gene.html @@ -246,7 +246,7 @@

Examples

## for subject 3 cowplot::plot_grid(plotlist = p_list, ncol = 2) } -#> 2024-03-28 14:39:19.22601 loading file /github/home/.cache/R/BiocFileCache/a7114b37d42_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-03-28 18:07:53.684839 loading file /github/home/.cache/R/BiocFileCache/a7153961056_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1