diff --git a/articles/TenX_data_download.html b/articles/TenX_data_download.html index 2553d940..2307b290 100644 --- a/articles/TenX_data_download.html +++ b/articles/TenX_data_download.html @@ -535,7 +535,7 @@
## Run our shiny app
if (interactive()) {
@@ -1117,9 +1117,9 @@ Reproducibilitylibrary("knitr")
knit("TenX_data_download.Rmd", tangle = TRUE)
Date the vignette was generated.
-#> [1] "2024-04-05 20:05:28 UTC"
+#> [1] "2024-04-05 20:07:28 UTC"
Wallclock time spent generating the vignette.
-#> Time difference of 1.781 mins
+#> Time difference of 1.79 mins
R
session information.
#> ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
#> setting value
diff --git a/articles/guide_to_spatial_registration.html b/articles/guide_to_spatial_registration.html
index f76bb9ca..1e1e8550 100644
--- a/articles/guide_to_spatial_registration.html
+++ b/articles/guide_to_spatial_registration.html
@@ -287,7 +287,7 @@ Spatial Reference
## get reference layer enrichment statistics
layer_modeling_results <- fetch_data(type = "modeling_results")
-#> 2024-04-05 20:05:47.05775 loading file /github/home/.cache/R/BiocFileCache/11592b032277_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
+#> 2024-04-05 20:07:48.06424 loading file /github/home/.cache/R/BiocFileCache/115b6b55de6b_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
layer_modeling_results$enrichment[1:5, 1:5]
#> t_stat_WM t_stat_Layer1 t_stat_Layer2 t_stat_Layer3 t_stat_Layer4
@@ -389,18 +389,18 @@ Get Enrichment statistics
gene_ensembl = "gene_id",
gene_name = "gene_name"
)
-#> 2024-04-05 20:05:54.605212 make pseudobulk object
-#> 2024-04-05 20:05:56.27116 dropping 13 pseudo-bulked samples that are below 'min_ncells'.
-#> 2024-04-05 20:05:56.330158 drop lowly expressed genes
-#> 2024-04-05 20:05:56.50757 normalize expression
-#> 2024-04-05 20:05:57.954918 create model matrix
-#> 2024-04-05 20:05:57.979144 run duplicateCorrelation()
-#> 2024-04-05 20:06:11.317145 The estimated correlation is: 0.138734774807097
-#> 2024-04-05 20:06:11.319783 computing enrichment statistics
-#> 2024-04-05 20:06:12.414152 extract and reformat enrichment results
-#> 2024-04-05 20:06:12.466076 running the baseline pairwise model
-#> 2024-04-05 20:06:12.622605 computing pairwise statistics
-#> 2024-04-05 20:06:13.930996 computing F-statistics
+#> 2024-04-05 20:07:55.729548 make pseudobulk object
+#> 2024-04-05 20:07:57.406807 dropping 13 pseudo-bulked samples that are below 'min_ncells'.
+#> 2024-04-05 20:07:57.468537 drop lowly expressed genes
+#> 2024-04-05 20:07:57.669501 normalize expression
+#> 2024-04-05 20:07:59.128324 create model matrix
+#> 2024-04-05 20:07:59.152507 run duplicateCorrelation()
+#> 2024-04-05 20:08:12.466311 The estimated correlation is: 0.138734774807097
+#> 2024-04-05 20:08:12.46879 computing enrichment statistics
+#> 2024-04-05 20:08:13.52675 extract and reformat enrichment results
+#> 2024-04-05 20:08:13.578985 running the baseline pairwise model
+#> 2024-04-05 20:08:13.754707 computing pairwise statistics
+#> 2024-04-05 20:08:15.065329 computing F-statistics
Date the vignette was generated.
-#> [1] "2024-04-05 20:06:15 UTC"
+#> [1] "2024-04-05 20:08:16 UTC"
Wallclock time spent generating the vignette.
-#> Time difference of 40.931 secs
+#> Time difference of 42.017 secs
R
session information.
#> ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
#> setting value
diff --git a/articles/multi_gene_plots.html b/articles/multi_gene_plots.html
index 74d2934a..4a0b5b92 100644
--- a/articles/multi_gene_plots.html
+++ b/articles/multi_gene_plots.html
@@ -197,9 +197,9 @@ Plotting One Gene
modeling_results <- fetch_data(type = "modeling_results")
-#> 2024-04-05 20:06:38.485929 loading file /github/home/.cache/R/BiocFileCache/11592b032277_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
+#> 2024-04-05 20:08:40.97899 loading file /github/home/.cache/R/BiocFileCache/115b6b55de6b_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
sce_layer <- fetch_data(type = "sce_layer")
-#> 2024-04-05 20:06:39.406176 loading file /github/home/.cache/R/BiocFileCache/11597ad98e84_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-04-05 20:08:42.230782 loading file /github/home/.cache/R/BiocFileCache/115b403d7ac1_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
sig_genes <- sig_genes_extract_all(
n = 400,
modeling_results = modeling_results,
@@ -423,9 +423,9 @@ Reproducibilitylibrary("knitr")
knit("multi_gene_plots.Rmd", tangle = TRUE)
Date the vignette was generated.
-#> [1] "2024-04-05 20:06:55 UTC"
+#> [1] "2024-04-05 20:08:58 UTC"
Wallclock time spent generating the vignette.
-#> Time difference of 36.951 secs
+#> Time difference of 38.808 secs
R
session information.
#> ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
#> setting value
diff --git a/articles/spatialLIBD.html b/articles/spatialLIBD.html
index cb683ee7..70b0b24e 100644
--- a/articles/spatialLIBD.html
+++ b/articles/spatialLIBD.html
@@ -417,7 +417,7 @@ Downloading the data with s
## Download the small example sce data
sce <- fetch_data(type = "sce_example", eh = ehub)
-#> 2024-04-05 20:07:11.47321 loading file /github/home/.cache/R/BiocFileCache/11593b8b56cb_sce_sub_for_vignette.Rdata%3Fdl%3D1
+#> 2024-04-05 20:09:15.429788 loading file /github/home/.cache/R/BiocFileCache/115b36d9e52_sce_sub_for_vignette.Rdata%3Fdl%3D1
## Convert to a SpatialExperiment object
spe <- sce_to_spe(sce)
@@ -429,9 +429,9 @@ Downloading the data with s
## Query ExperimentHub and download the data
if (!exists("sce_layer")) sce_layer <- fetch_data(type = "sce_layer", eh = ehub)
-#> 2024-04-05 20:07:15.965327 loading file /github/home/.cache/R/BiocFileCache/11597ad98e84_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-04-05 20:09:21.29669 loading file /github/home/.cache/R/BiocFileCache/115b403d7ac1_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
modeling_results <- fetch_data("modeling_results", eh = ehub)
-#> 2024-04-05 20:07:16.409124 loading file /github/home/.cache/R/BiocFileCache/11592b032277_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
+#> 2024-04-05 20:09:21.747998 loading file /github/home/.cache/R/BiocFileCache/115b6b55de6b_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
Once you have downloaded the objects, we can explore them a little
bit
@@ -504,7 +504,7 @@ Downloading the data with s
)
)
#> user system elapsed
-#> 9.855 0.432 10.306
+#> 9.888 0.484 10.381
## Explore the result
class(sig_genes)
@@ -1380,9 +1380,9 @@ Reproducibilitylibrary("knitr")
knit("spatialLIBD.Rmd", tangle = TRUE)
Date the vignette was generated.
-#> [1] "2024-04-05 20:07:34 UTC"
+#> [1] "2024-04-05 20:09:39 UTC"
Wallclock time spent generating the vignette.
-#> Time difference of 35.419 secs
+#> Time difference of 37.369 secs
R
session information.
#> ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
#> setting value
diff --git a/index.html b/index.html
index 26dedc9b..04a80f0d 100644
--- a/index.html
+++ b/index.html
@@ -539,7 +539,7 @@ Dev status
-
+
diff --git a/pkgdown.yml b/pkgdown.yml
index cee0dc65..865d58f0 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -6,5 +6,5 @@ articles:
guide_to_spatial_registration: guide_to_spatial_registration.html
multi_gene_plots: multi_gene_plots.html
spatialLIBD: spatialLIBD.html
-last_built: 2024-04-05T19:58Z
+last_built: 2024-04-05T19:59Z
diff --git a/reference/add_images.html b/reference/add_images.html
index 3f3acdb1..a1825593 100644
--- a/reference/add_images.html
+++ b/reference/add_images.html
@@ -165,29 +165,29 @@ Examples
image_paths = c("151507" = "https://spatial-dlpfc.s3.us-east-2.amazonaws.com/images/151507_tissue_lowres_image.png")
))
}
-#> 2024-04-05 19:58:24.996743 loading file /github/home/.cache/R/BiocFileCache/155f98a302_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
-#> 2024-04-05 19:58:40.609337 adding image for sample 151507
-#> 2024-04-05 19:58:41.338532 adding image for sample 151508
+#> 2024-04-05 20:00:03.124019 loading file /github/home/.cache/R/BiocFileCache/1560561f15f7_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-04-05 20:00:19.145376 adding image for sample 151507
+#> 2024-04-05 20:00:20.898775 adding image for sample 151508
#> Warning: No image was found for sample: 151508
-#> 2024-04-05 19:58:41.338855 adding image for sample 151509
+#> 2024-04-05 20:00:20.899117 adding image for sample 151509
#> Warning: No image was found for sample: 151509
-#> 2024-04-05 19:58:41.339072 adding image for sample 151510
+#> 2024-04-05 20:00:20.899331 adding image for sample 151510
#> Warning: No image was found for sample: 151510
-#> 2024-04-05 19:58:41.339273 adding image for sample 151669
+#> 2024-04-05 20:00:20.899534 adding image for sample 151669
#> Warning: No image was found for sample: 151669
-#> 2024-04-05 19:58:41.339472 adding image for sample 151670
+#> 2024-04-05 20:00:20.899734 adding image for sample 151670
#> Warning: No image was found for sample: 151670
-#> 2024-04-05 19:58:41.339661 adding image for sample 151671
+#> 2024-04-05 20:00:20.899927 adding image for sample 151671
#> Warning: No image was found for sample: 151671
-#> 2024-04-05 19:58:41.339851 adding image for sample 151672
+#> 2024-04-05 20:00:20.900118 adding image for sample 151672
#> Warning: No image was found for sample: 151672
-#> 2024-04-05 19:58:41.340041 adding image for sample 151673
+#> 2024-04-05 20:00:20.900309 adding image for sample 151673
#> Warning: No image was found for sample: 151673
-#> 2024-04-05 19:58:41.340232 adding image for sample 151674
+#> 2024-04-05 20:00:20.900553 adding image for sample 151674
#> Warning: No image was found for sample: 151674
-#> 2024-04-05 19:58:41.340424 adding image for sample 151675
+#> 2024-04-05 20:00:20.900764 adding image for sample 151675
#> Warning: No image was found for sample: 151675
-#> 2024-04-05 19:58:41.340619 adding image for sample 151676
+#> 2024-04-05 20:00:20.900966 adding image for sample 151676
#> Warning: No image was found for sample: 151676
#> DataFrame with 13 rows and 4 columns
#> sample_id image_id data scaleFactor
diff --git a/reference/add_key.html b/reference/add_key.html
index 52f8800e..d072b0d1 100644
--- a/reference/add_key.html
+++ b/reference/add_key.html
@@ -117,7 +117,7 @@ Examples
## Note that the original 'key' order was 'sample_id'_'barcode' and we'
## have since changed it to 'barcode'_'sample_id'.
}
-#> 2024-04-05 19:58:43.40326 loading file /github/home/.cache/R/BiocFileCache/155f98a302_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-04-05 20:00:23.587719 loading file /github/home/.cache/R/BiocFileCache/1560561f15f7_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
#> [1] "AAACAACGAATAGTTC-1_151507" "AAACAAGTATCTCCCA-1_151507"
#> [3] "AAACAATCTACTAGCA-1_151507" "AAACACCAATAACTGC-1_151507"
#> [5] "AAACAGCTTTCAGAAG-1_151507" "AAACAGGGTCTATATT-1_151507"
diff --git a/reference/annotate_registered_clusters.html b/reference/annotate_registered_clusters.html
index 04d383e3..675dba5c 100644
--- a/reference/annotate_registered_clusters.html
+++ b/reference/annotate_registered_clusters.html
@@ -139,7 +139,7 @@ Examples
if (!exists("modeling_results")) {
modeling_results <- fetch_data(type = "modeling_results")
}
-#> 2024-04-05 19:58:57.92285 loading file /github/home/.cache/R/BiocFileCache/11592b032277_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
+#> 2024-04-05 20:00:38.680408 loading file /github/home/.cache/R/BiocFileCache/115b6b55de6b_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
## Compute the correlations
cor_stats_layer <- layer_stat_cor(
diff --git a/reference/check_modeling_results.html b/reference/check_modeling_results.html
index ceb0500b..e34e931c 100644
--- a/reference/check_modeling_results.html
+++ b/reference/check_modeling_results.html
@@ -108,7 +108,7 @@ Examples
if (!exists("modeling_results")) {
modeling_results <- fetch_data(type = "modeling_results")
}
-#> 2024-04-05 19:58:58.831466 loading file /github/home/.cache/R/BiocFileCache/11592b032277_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
+#> 2024-04-05 20:00:40.02132 loading file /github/home/.cache/R/BiocFileCache/115b6b55de6b_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
## Check the object
xx <- check_modeling_results(modeling_results)
diff --git a/reference/check_sce.html b/reference/check_sce.html
index b52ee553..cdb461eb 100644
--- a/reference/check_sce.html
+++ b/reference/check_sce.html
@@ -131,7 +131,7 @@ Examples
## Check the object
check_sce(sce_example)
}
-#> 2024-04-05 19:58:59.752855 loading file /github/home/.cache/R/BiocFileCache/11593b8b56cb_sce_sub_for_vignette.Rdata%3Fdl%3D1
+#> 2024-04-05 20:00:41.402931 loading file /github/home/.cache/R/BiocFileCache/115b36d9e52_sce_sub_for_vignette.Rdata%3Fdl%3D1
#> class: SingleCellExperiment
#> dim: 33538 47681
#> metadata(1): image
diff --git a/reference/check_sce_layer.html b/reference/check_sce_layer.html
index f4976477..fbd35244 100644
--- a/reference/check_sce_layer.html
+++ b/reference/check_sce_layer.html
@@ -111,7 +111,7 @@ Examples
## Obtain the necessary data
if (!exists("sce_layer")) sce_layer <- fetch_data("sce_layer")
-#> 2024-04-05 19:59:02.128027 loading file /github/home/.cache/R/BiocFileCache/11597ad98e84_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-04-05 20:00:44.308081 loading file /github/home/.cache/R/BiocFileCache/115b403d7ac1_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
## Check the object
check_sce_layer(sce_layer)
diff --git a/reference/check_spe.html b/reference/check_spe.html
index 2ca1a131..bfe7894d 100644
--- a/reference/check_spe.html
+++ b/reference/check_spe.html
@@ -123,7 +123,7 @@ Examples
## Check the object
check_spe(spe)
}
-#> 2024-04-05 19:59:03.978877 loading file /github/home/.cache/R/BiocFileCache/155f98a302_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-04-05 20:00:46.59603 loading file /github/home/.cache/R/BiocFileCache/1560561f15f7_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
#> class: SpatialExperiment
#> dim: 33538 47681
#> metadata(0):
diff --git a/reference/cluster_export.html b/reference/cluster_export.html
index 5a272448..3ad3954b 100644
--- a/reference/cluster_export.html
+++ b/reference/cluster_export.html
@@ -134,7 +134,7 @@ Examples
cluster_export(spe, "spatialLIBD")
cluster_export(spe, "GraphBased")
}
-#> 2024-04-05 19:59:18.470286 loading file /github/home/.cache/R/BiocFileCache/155f98a302_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-04-05 20:01:01.877567 loading file /github/home/.cache/R/BiocFileCache/1560561f15f7_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
#> Overwriting 'spe$key'. Set 'overwrite = FALSE' if you do not want to overwrite it.
#> Overwriting 'spe$key'. Set 'overwrite = FALSE' if you do not want to overwrite it.
diff --git a/reference/cluster_import.html b/reference/cluster_import.html
index 09c988d2..c87c23e3 100644
--- a/reference/cluster_import.html
+++ b/reference/cluster_import.html
@@ -137,11 +137,11 @@ Examples
## Re-import them
colData(cluster_import(spe))
}
-#> 2024-04-05 19:59:32.667595 loading file /github/home/.cache/R/BiocFileCache/155f98a302_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-04-05 20:01:16.840454 loading file /github/home/.cache/R/BiocFileCache/1560561f15f7_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
#> Overwriting 'spe$key'. Set 'overwrite = FALSE' if you do not want to overwrite it.
-#> Warning: '/tmp/RtmpgLjxXM/exported_clusters/spatialLIBD' already exists
+#> Warning: '/tmp/Rtmpl5MUOg/exported_clusters/spatialLIBD' already exists
#> Overwriting 'spe$key'. Set 'overwrite = FALSE' if you do not want to overwrite it.
-#> Warning: '/tmp/RtmpgLjxXM/exported_clusters/GraphBased' already exists
+#> Warning: '/tmp/Rtmpl5MUOg/exported_clusters/GraphBased' already exists
#> Overwriting 'spe$key'. Set 'overwrite = FALSE' if you do not want to overwrite it.
#> DataFrame with 47681 rows and 71 columns
#> key sample_id Cluster sum_umi
diff --git a/reference/fetch_data.html b/reference/fetch_data.html
index a2a133b7..02a2f14a 100644
--- a/reference/fetch_data.html
+++ b/reference/fetch_data.html
@@ -165,7 +165,7 @@ Examples
## Download the SingleCellExperiment object
## at the layer-level
if (!exists("sce_layer")) sce_layer <- fetch_data("sce_layer")
-#> 2024-04-05 19:59:47.859114 loading file /github/home/.cache/R/BiocFileCache/11597ad98e84_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-04-05 20:01:33.003093 loading file /github/home/.cache/R/BiocFileCache/115b403d7ac1_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
## Explore the data
sce_layer
diff --git a/reference/frame_limits.html b/reference/frame_limits.html
index 216bbc70..283b75a6 100644
--- a/reference/frame_limits.html
+++ b/reference/frame_limits.html
@@ -154,7 +154,7 @@ Examples
## Obtain the frame limits for one sample
frame_limits(spe, sampleid = "151673")
}
-#> 2024-04-05 19:59:49.476695 loading file /github/home/.cache/R/BiocFileCache/155f98a302_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-04-05 20:01:35.173933 loading file /github/home/.cache/R/BiocFileCache/1560561f15f7_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
#> $y_min
#> [1] 64
#>
diff --git a/reference/gene_set_enrichment.html b/reference/gene_set_enrichment.html
index 5bc094c7..afbfa05c 100644
--- a/reference/gene_set_enrichment.html
+++ b/reference/gene_set_enrichment.html
@@ -176,7 +176,7 @@ Examples
if (!exists("modeling_results")) {
modeling_results <- fetch_data(type = "modeling_results")
}
-#> 2024-04-05 20:00:04.267055 loading file /github/home/.cache/R/BiocFileCache/11592b032277_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
+#> 2024-04-05 20:01:50.66524 loading file /github/home/.cache/R/BiocFileCache/115b6b55de6b_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
## Compute the gene set enrichment results
asd_sfari_enrichment <- gene_set_enrichment(
diff --git a/reference/gene_set_enrichment_plot.html b/reference/gene_set_enrichment_plot.html
index a2a1503e..a165053d 100644
--- a/reference/gene_set_enrichment_plot.html
+++ b/reference/gene_set_enrichment_plot.html
@@ -178,7 +178,7 @@ Examples
if (!exists("modeling_results")) {
modeling_results <- fetch_data(type = "modeling_results")
}
-#> 2024-04-05 20:00:05.476083 loading file /github/home/.cache/R/BiocFileCache/11592b032277_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
+#> 2024-04-05 20:01:52.315443 loading file /github/home/.cache/R/BiocFileCache/115b6b55de6b_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
## Compute the gene set enrichment results
asd_sfari_enrichment <- gene_set_enrichment(
diff --git a/reference/geom_spatial.html b/reference/geom_spatial.html
index 5665d87a..ee9c0d4b 100644
--- a/reference/geom_spatial.html
+++ b/reference/geom_spatial.html
@@ -175,7 +175,7 @@ Examples
## Clean up
rm(spe_sub)
}
-#> 2024-04-05 20:00:07.238809 loading file /github/home/.cache/R/BiocFileCache/155f98a302_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-04-05 20:01:54.538708 loading file /github/home/.cache/R/BiocFileCache/1560561f15f7_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
diff --git a/reference/get_colors.html b/reference/get_colors.html
index 823b5d7d..d1437cd4 100644
--- a/reference/get_colors.html
+++ b/reference/get_colors.html
@@ -105,7 +105,7 @@ Examples
## Obtain the necessary data
if (!exists("sce_layer")) sce_layer <- fetch_data("sce_layer")
-#> 2024-04-05 20:00:22.551161 loading file /github/home/.cache/R/BiocFileCache/11597ad98e84_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-04-05 20:02:10.842966 loading file /github/home/.cache/R/BiocFileCache/115b403d7ac1_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
## Example layer colors with the corresponding names
get_colors(libd_layer_colors, sce_layer$layer_guess)
diff --git a/reference/img_edit.html b/reference/img_edit.html
index 18742337..cc29ddff 100644
--- a/reference/img_edit.html
+++ b/reference/img_edit.html
@@ -222,7 +222,7 @@ Examples
x <- img_edit(spe, sampleid = "151507", brightness = 25)
plot(x)
}
-#> 2024-04-05 20:00:23.635238 loading file /github/home/.cache/R/BiocFileCache/155f98a302_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-04-05 20:02:12.361915 loading file /github/home/.cache/R/BiocFileCache/1560561f15f7_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
diff --git a/reference/img_update.html b/reference/img_update.html
index f01a72ed..b02ce585 100644
--- a/reference/img_update.html
+++ b/reference/img_update.html
@@ -139,7 +139,7 @@ Examples
## Reduce brightness to 25% and update the imgData()
imgData(img_update(spe, sampleid = "151507", brightness = 25))
}
-#> 2024-04-05 20:00:39.204887 loading file /github/home/.cache/R/BiocFileCache/155f98a302_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-04-05 20:02:28.610867 loading file /github/home/.cache/R/BiocFileCache/1560561f15f7_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
#> DataFrame with 13 rows and 4 columns
#> sample_id image_id data scaleFactor
#> <character> <character> <list> <numeric>
diff --git a/reference/img_update_all.html b/reference/img_update_all.html
index e84bb674..b9e2c6f9 100644
--- a/reference/img_update_all.html
+++ b/reference/img_update_all.html
@@ -138,7 +138,7 @@ Examples
## update the imgData()
imgData(img_update_all(spe, brightness = 25))
}
-#> 2024-04-05 20:00:53.415044 loading file /github/home/.cache/R/BiocFileCache/155f98a302_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-04-05 20:02:43.333119 loading file /github/home/.cache/R/BiocFileCache/1560561f15f7_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
#> DataFrame with 24 rows and 4 columns
#> sample_id image_id data scaleFactor
#> <character> <character> <list> <numeric>
diff --git a/reference/layer_boxplot.html b/reference/layer_boxplot.html
index 2678b8e3..cbc40a03 100644
--- a/reference/layer_boxplot.html
+++ b/reference/layer_boxplot.html
@@ -185,9 +185,9 @@ Examples
if (!exists("modeling_results")) {
modeling_results <- fetch_data(type = "modeling_results")
}
-#> 2024-04-05 20:01:10.230575 loading file /github/home/.cache/R/BiocFileCache/11592b032277_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
+#> 2024-04-05 20:03:00.531552 loading file /github/home/.cache/R/BiocFileCache/115b6b55de6b_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
if (!exists("sce_layer")) sce_layer <- fetch_data(type = "sce_layer")
-#> 2024-04-05 20:01:11.073344 loading file /github/home/.cache/R/BiocFileCache/11597ad98e84_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-04-05 20:03:01.79801 loading file /github/home/.cache/R/BiocFileCache/115b403d7ac1_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
## Top 2 genes from the enrichment model
sig_genes <- sig_genes_extract_all(
diff --git a/reference/layer_stat_cor.html b/reference/layer_stat_cor.html
index 708fc7d0..93eeacac 100644
--- a/reference/layer_stat_cor.html
+++ b/reference/layer_stat_cor.html
@@ -156,7 +156,7 @@ Examples
if (!exists("modeling_results")) {
modeling_results <- fetch_data(type = "modeling_results")
}
-#> 2024-04-05 20:01:14.179337 loading file /github/home/.cache/R/BiocFileCache/11592b032277_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
+#> 2024-04-05 20:03:05.811506 loading file /github/home/.cache/R/BiocFileCache/115b6b55de6b_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
## Compute the correlations
cor_stats_layer <- layer_stat_cor(
diff --git a/reference/layer_stat_cor_plot.html b/reference/layer_stat_cor_plot.html
index 010966e5..6a50ede7 100644
--- a/reference/layer_stat_cor_plot.html
+++ b/reference/layer_stat_cor_plot.html
@@ -145,7 +145,7 @@ Examples
if (!exists("modeling_results")) {
modeling_results <- fetch_data(type = "modeling_results")
}
-#> 2024-04-05 20:01:15.199864 loading file /github/home/.cache/R/BiocFileCache/11592b032277_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
+#> 2024-04-05 20:03:07.277842 loading file /github/home/.cache/R/BiocFileCache/115b6b55de6b_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
## Compute the correlations
cor_stats_layer <- layer_stat_cor(
diff --git a/reference/registration_block_cor.html b/reference/registration_block_cor.html
index 98d1c584..63aa1503 100644
--- a/reference/registration_block_cor.html
+++ b/reference/registration_block_cor.html
@@ -146,9 +146,9 @@ Examples
#>
#> rgstr_> ## Pseudo-bulk
#> rgstr_> sce_pseudo <- registration_pseudobulk(sce, "Cell_Cycle", "sample_id", c("age"), min_ncells = NULL)
-#> 2024-04-05 20:01:17.209751 make pseudobulk object
-#> 2024-04-05 20:01:18.270705 drop lowly expressed genes
-#> 2024-04-05 20:01:18.342654 normalize expression
+#> 2024-04-05 20:03:09.307972 make pseudobulk object
+#> 2024-04-05 20:03:10.369723 drop lowly expressed genes
+#> 2024-04-05 20:03:10.443448 normalize expression
#>
#> rgstr_> colData(sce_pseudo)
#> DataFrame with 20 rows and 8 columns
@@ -180,7 +180,7 @@ Examples
#> E_S S E 11
#>
#> rgstr_> registration_mod <- registration_model(sce_pseudo, "age")
-#> 2024-04-05 20:01:18.422912 create model matrix
+#> 2024-04-05 20:03:10.525761 create model matrix
#>
#> rgstr_> head(registration_mod)
#> registration_variableG0 registration_variableG1 registration_variableG2M
@@ -198,8 +198,8 @@ Examples
#> E_G0 0 20.97006
#> A_G1 0 19.18719
block_cor <- registration_block_cor(sce_pseudo, registration_mod)
-#> 2024-04-05 20:01:18.435945 run duplicateCorrelation()
-#> 2024-04-05 20:01:19.750538 The estimated correlation is: -0.0187869166526901
+#> 2024-04-05 20:03:10.540396 run duplicateCorrelation()
+#> 2024-04-05 20:03:11.833898 The estimated correlation is: -0.0187869166526901
diff --git a/reference/registration_model.html b/reference/registration_model.html
index d3587404..5cdb99ef 100644
--- a/reference/registration_model.html
+++ b/reference/registration_model.html
@@ -148,9 +148,9 @@