From 57fc1b1b45f88b485274bfdaef60c34f93b9c7a3 Mon Sep 17 00:00:00 2001 From: lcolladotor Date: Fri, 24 May 2024 06:39:35 +0000 Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20LieberIn?= =?UTF-8?q?stitute/spatialLIBD@45b22bcf2a9c2b701e4ea7bf296921a36a998dad=20?= =?UTF-8?q?=F0=9F=9A=80?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- articles/TenX_data_download.html | 20 ++++++------- articles/guide_to_spatial_registration.html | 30 ++++++++++---------- articles/multi_gene_plots.html | 8 +++--- articles/spatialLIBD.html | 12 ++++---- pkgdown.yml | 2 +- reference/add_images.html | 26 ++++++++--------- reference/add_key.html | 2 +- reference/annotate_registered_clusters.html | 2 +- reference/check_modeling_results.html | 2 +- reference/check_sce.html | 2 +- reference/check_sce_layer.html | 2 +- reference/check_spe.html | 2 +- reference/cluster_export.html | 2 +- reference/cluster_import.html | 6 ++-- reference/fetch_data.html | 2 +- reference/frame_limits.html | 2 +- reference/gene_set_enrichment.html | 2 +- reference/gene_set_enrichment_plot.html | 2 +- reference/geom_spatial.html | 2 +- reference/get_colors.html | 2 +- reference/img_edit.html | 2 +- reference/img_update.html | 2 +- reference/img_update_all.html | 2 +- reference/layer_boxplot.html | 4 +-- reference/layer_stat_cor.html | 2 +- reference/layer_stat_cor_plot.html | 2 +- reference/registration_block_cor.html | 12 ++++---- reference/registration_model.html | 8 +++--- reference/registration_pseudobulk.html | 6 ++-- reference/registration_stats_anova.html | 18 ++++++------ reference/registration_stats_enrichment.html | 20 ++++++------- reference/registration_stats_pairwise.html | 20 ++++++------- reference/registration_wrapper.html | 24 ++++++++-------- reference/sce_to_spe.html | 2 +- reference/sig_genes_extract.html | 4 +-- reference/sig_genes_extract_all.html | 4 +-- reference/vis_clus.html | 2 +- reference/vis_clus_p.html | 2 +- reference/vis_gene.html | 2 +- reference/vis_gene_p.html | 2 +- reference/vis_grid_clus.html | 2 +- reference/vis_grid_gene.html | 2 +- 42 files changed, 137 insertions(+), 137 deletions(-) diff --git a/articles/TenX_data_download.html b/articles/TenX_data_download.html index bb0bfd4d..7c376f72 100644 --- a/articles/TenX_data_download.html +++ b/articles/TenX_data_download.html @@ -537,8 +537,8 @@

From Gencode## Show the GTF cache location gtf_cache -#> BFC4 -#> "/github/home/.cache/R/BiocFileCache/68fe24c4821c_gencode.v32.annotation.gtf.gz" +#> BFC4 +#> "/github/home/.cache/R/BiocFileCache/272603ecd3b_gencode.v32.annotation.gtf.gz" 
 
 ## Import into R (takes ~1 min)
@@ -832,11 +832,11 @@ 
Wrapper functions= c("lowres", "hires", "detected", "aligned"), load = TRUE,
     reference_gtf = gtf_cache
 )
-#> 2024-05-24 05:56:03.512447 SpatialExperiment::read10xVisium: reading basic data from SpaceRanger
-#> 2024-05-24 05:56:14.467328 read10xVisiumAnalysis: reading analysis output from SpaceRanger
-#> 2024-05-24 05:56:15.523564 add10xVisiumAnalysis: adding analysis output from SpaceRanger
-#> 2024-05-24 05:56:15.776144 rtracklayer::import: reading the reference GTF file
-#> 2024-05-24 05:56:42.003628 adding gene information to the SPE object
+#> 2024-05-24 06:38:38.834715 SpatialExperiment::read10xVisium: reading basic data from SpaceRanger
+#> 2024-05-24 06:38:49.341463 read10xVisiumAnalysis: reading analysis output from SpaceRanger
+#> 2024-05-24 06:38:50.315964 add10xVisiumAnalysis: adding analysis output from SpaceRanger
+#> 2024-05-24 06:38:50.555229 rtracklayer::import: reading the reference GTF file
+#> 2024-05-24 06:39:16.039132 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()
@@ -844,7 +844,7 @@ 
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.
-#> 2024-05-24 05:56:43.541219 adding information used by spatialLIBD
+#> 2024-05-24 06:39:17.472739 adding information used by spatialLIBD 
 ## Run our shiny app
 if (interactive()) {
@@ -1128,9 +1128,9 @@ 
Reproducibilitylibrary("knitr")
 knit("TenX_data_download.Rmd", tangle = TRUE)

Date the vignette was generated.

-
#> [1] "2024-05-24 05:56:44 UTC"
+
#> [1] "2024-05-24 06:39:18 UTC"

Wallclock time spent generating the vignette.

-
#> Time difference of 1.771 mins
+
#> Time difference of 1.689 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 680fc23a..1a2daeee 100644
--- a/articles/guide_to_spatial_registration.html
+++ b/articles/guide_to_spatial_registration.html
@@ -286,7 +286,7 @@ 
Spatial Reference
 ## get reference layer enrichment statistics
 layer_modeling_results <- fetch_data(type = "modeling_results")
-#> 2024-05-24 05:53:03.171681 loading file /github/home/.cache/R/BiocFileCache/68fe5f60223e_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1

+#> 2024-05-24 06:35:47.047988 loading file /github/home/.cache/R/BiocFileCache/2723d218943_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
 
 layer_modeling_results$enrichment[1:5, 1:5]
@@ -389,18 +389,18 @@ 
Get Enrichment statistics
     gene_ensembl = "gene_id",
     gene_name = "gene_name"
 )
-#> 2024-05-24 05:53:11.500453 make pseudobulk object
-#> 2024-05-24 05:53:13.159878 dropping 13 pseudo-bulked samples that are below 'min_ncells'.
-#> 2024-05-24 05:53:13.216625 drop lowly expressed genes
-#> 2024-05-24 05:53:13.375066 normalize expression
-#> 2024-05-24 05:53:14.113209 create model matrix
-#> 2024-05-24 05:53:14.137484 run duplicateCorrelation()
-#> 2024-05-24 05:53:27.872322 The estimated correlation is: 0.138734774807097
-#> 2024-05-24 05:53:27.874945 computing enrichment statistics
-#> 2024-05-24 05:53:28.940318 extract and reformat enrichment results
-#> 2024-05-24 05:53:28.995866 running the baseline pairwise model
-#> 2024-05-24 05:53:29.157696 computing pairwise statistics
-#> 2024-05-24 05:53:30.510306 computing F-statistics
+#> 2024-05-24 06:35:55.431226 make pseudobulk object +#> 2024-05-24 06:35:57.076661 dropping 13 pseudo-bulked samples that are below 'min_ncells'. +#> 2024-05-24 06:35:57.133294 drop lowly expressed genes +#> 2024-05-24 06:35:57.293617 normalize expression +#> 2024-05-24 06:35:58.019479 create model matrix +#> 2024-05-24 06:35:58.043371 run duplicateCorrelation() +#> 2024-05-24 06:36:11.79821 The estimated correlation is: 0.138734774807097 +#> 2024-05-24 06:36:11.800817 computing enrichment statistics +#> 2024-05-24 06:36:12.902637 extract and reformat enrichment results +#> 2024-05-24 06:36:12.957636 running the baseline pairwise model +#> 2024-05-24 06:36:13.119462 computing pairwise statistics +#> 2024-05-24 06:36:14.444971 computing F-statistics

Extract Enrichment t-statistics @@ -561,9 +561,9 @@

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

Date the vignette was generated.

-
#> [1] "2024-05-24 05:53:31 UTC"
+
#> [1] "2024-05-24 06:36:15 UTC"

Wallclock time spent generating the vignette.

-
#> Time difference of 40.167 secs
+
#> Time difference of 40.343 secs

R session information.

#> ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
 #>  setting  value
diff --git a/articles/multi_gene_plots.html b/articles/multi_gene_plots.html
index 691fbe80..63b1dc90 100644
--- a/articles/multi_gene_plots.html
+++ b/articles/multi_gene_plots.html
@@ -197,10 +197,10 @@ 
Plotting One Gene
 modeling_results <- fetch_data(type = "modeling_results")
-#> 2024-05-24 05:53:55.10797 loading file /github/home/.cache/R/BiocFileCache/68fe5f60223e_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1

+#> 2024-05-24 06:36:38.7652 loading file /github/home/.cache/R/BiocFileCache/2723d218943_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
 sce_layer <- fetch_data(type = "sce_layer")
-#> 2024-05-24 05:53:56.055565 loading file /github/home/.cache/R/BiocFileCache/68fe3214d83_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-05-24 06:36:39.654834 loading file /github/home/.cache/R/BiocFileCache/272335c9fe4_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1 
 sig_genes <- sig_genes_extract_all(
     n = 400,
@@ -426,9 +426,9 @@ 
Reproducibilitylibrary("knitr")
 knit("multi_gene_plots.Rmd", tangle = TRUE)

Date the vignette was generated.

-
#> [1] "2024-05-24 05:54:12 UTC"
+
#> [1] "2024-05-24 06:36:55 UTC"

Wallclock time spent generating the vignette.

-
#> Time difference of 37.577 secs
+
#> Time difference of 36.694 secs

R session information.

#> ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
 #>  setting  value
diff --git a/articles/spatialLIBD.html b/articles/spatialLIBD.html
index 015ade2f..7d4fc649 100644
--- a/articles/spatialLIBD.html
+++ b/articles/spatialLIBD.html
@@ -416,7 +416,7 @@ 
Downloading the data with s
 
 ## Download the small example sce data
 sce <- fetch_data(type = "sce_example", eh = ehub)
-#> 2024-05-24 05:54:29.419322 loading file /github/home/.cache/R/BiocFileCache/68fe1fbace58_sce_sub_for_vignette.Rdata%3Fdl%3D1

+#> 2024-05-24 06:37:10.851743 loading file /github/home/.cache/R/BiocFileCache/2724577c975_sce_sub_for_vignette.Rdata%3Fdl%3D1
 
 ## Convert to a SpatialExperiment object
@@ -429,10 +429,10 @@ 
Downloading the data with s
 
 ## Query ExperimentHub and download the data
 if (!exists("sce_layer")) sce_layer <- fetch_data(type = "sce_layer", eh = ehub)
-#> 2024-05-24 05:54:34.28726 loading file /github/home/.cache/R/BiocFileCache/68fe3214d83_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-05-24 06:37:15.078541 loading file /github/home/.cache/R/BiocFileCache/272335c9fe4_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1 
 modeling_results <- fetch_data("modeling_results", eh = ehub)
-#> 2024-05-24 05:54:34.811874 loading file /github/home/.cache/R/BiocFileCache/68fe5f60223e_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
+#> 2024-05-24 06:37:15.54428 loading file /github/home/.cache/R/BiocFileCache/2723d218943_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1

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

@@ -509,7 +509,7 @@ 
Downloading the data with s
         )
 )
 #>    user  system elapsed 
-#>   9.890   0.360  10.267
+#> 9.311 0.272 9.616 
 
 ## Explore the result
@@ -1393,9 +1393,9 @@ 
Reproducibilitylibrary("knitr")
 knit("spatialLIBD.Rmd", tangle = TRUE)

Date the vignette was generated.

-
#> [1] "2024-05-24 05:54:53 UTC"
+
#> [1] "2024-05-24 06:37:33 UTC"

Wallclock time spent generating the vignette.

-
#> Time difference of 37.334 secs
+
#> Time difference of 34.326 secs

R session information.

#> ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
 #>  setting  value
diff --git a/pkgdown.yml b/pkgdown.yml
index dc5361ab..5f7a468f 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -6,5 +6,5 @@ articles:
   multi_gene_plots: multi_gene_plots.html
   spatialLIBD: spatialLIBD.html
   TenX_data_download: TenX_data_download.html
-last_built: 2024-05-24T05:47Z
+last_built: 2024-05-24T06:30Z
 
diff --git a/reference/add_images.html b/reference/add_images.html
index 2dc5d69f..388045f4 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")
     ))
 }
-#> 2024-05-24 05:47:24.123269 loading file /github/home/.cache/R/BiocFileCache/73cc5931d8b1_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
-#> 2024-05-24 05:47:40.0197 adding image for sample 151507
-#> 2024-05-24 05:47:40.959436 adding image for sample 151508
+#> 2024-05-24 06:30:16.330822 loading file /github/home/.cache/R/BiocFileCache/d401e78709e_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-05-24 06:30:31.752493 adding image for sample 151507
+#> 2024-05-24 06:30:32.539664 adding image for sample 151508
 #> Warning: No image was found for sample: 151508
-#> 2024-05-24 05:47:40.959802 adding image for sample 151509
+#> 2024-05-24 06:30:32.539975 adding image for sample 151509
 #> Warning: No image was found for sample: 151509
-#> 2024-05-24 05:47:40.960015 adding image for sample 151510
+#> 2024-05-24 06:30:32.540186 adding image for sample 151510
 #> Warning: No image was found for sample: 151510
-#> 2024-05-24 05:47:40.960216 adding image for sample 151669
+#> 2024-05-24 06:30:32.540384 adding image for sample 151669
 #> Warning: No image was found for sample: 151669
-#> 2024-05-24 05:47:40.960412 adding image for sample 151670
+#> 2024-05-24 06:30:32.540574 adding image for sample 151670
 #> Warning: No image was found for sample: 151670
-#> 2024-05-24 05:47:40.96062 adding image for sample 151671
+#> 2024-05-24 06:30:32.540765 adding image for sample 151671
 #> Warning: No image was found for sample: 151671
-#> 2024-05-24 05:47:40.960842 adding image for sample 151672
+#> 2024-05-24 06:30:32.540953 adding image for sample 151672
 #> Warning: No image was found for sample: 151672
-#> 2024-05-24 05:47:40.961048 adding image for sample 151673
+#> 2024-05-24 06:30:32.54114 adding image for sample 151673
 #> Warning: No image was found for sample: 151673
-#> 2024-05-24 05:47:40.961247 adding image for sample 151674
+#> 2024-05-24 06:30:32.541329 adding image for sample 151674
 #> Warning: No image was found for sample: 151674
-#> 2024-05-24 05:47:40.961457 adding image for sample 151675
+#> 2024-05-24 06:30:32.541521 adding image for sample 151675
 #> Warning: No image was found for sample: 151675
-#> 2024-05-24 05:47:40.961656 adding image for sample 151676
+#> 2024-05-24 06:30:32.541736 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 447828b7..b3d9bf49 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'.
 }
-#> 2024-05-24 05:47:43.671042 loading file /github/home/.cache/R/BiocFileCache/73cc5931d8b1_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-05-24 06:30:34.808823 loading file /github/home/.cache/R/BiocFileCache/d401e78709e_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 9c29abab..eec7513d 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")
 }
-#> 2024-05-24 05:47:58.457008 loading file /github/home/.cache/R/BiocFileCache/68fe5f60223e_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
+#> 2024-05-24 06:30:49.018547 loading file /github/home/.cache/R/BiocFileCache/2723d218943_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 126bca5a..d64a35c8 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")
 }
-#> 2024-05-24 05:47:59.670248 loading file /github/home/.cache/R/BiocFileCache/68fe5f60223e_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
+#> 2024-05-24 06:30:50.116349 loading file /github/home/.cache/R/BiocFileCache/2723d218943_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 fcfac579..35deb302 100644
--- a/reference/check_sce.html
+++ b/reference/check_sce.html
@@ -131,7 +131,7 @@ 
Examples

     ## Check the object
     check_sce(sce_example)
 }
-#> 2024-05-24 05:48:00.838924 loading file /github/home/.cache/R/BiocFileCache/68fe1fbace58_sce_sub_for_vignette.Rdata%3Fdl%3D1
+#> 2024-05-24 06:30:51.164432 loading file /github/home/.cache/R/BiocFileCache/2724577c975_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 020b8e0c..8e337e69 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")
-#> 2024-05-24 05:48:03.668919 loading file /github/home/.cache/R/BiocFileCache/68fe3214d83_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-05-24 06:30:53.653019 loading file /github/home/.cache/R/BiocFileCache/272335c9fe4_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 6cc57220..fb50748b 100644
--- a/reference/check_spe.html
+++ b/reference/check_spe.html
@@ -123,7 +123,7 @@ 
Examples

     ## Check the object
     check_spe(spe)
 }
-#> 2024-05-24 05:48:05.006384 loading file /github/home/.cache/R/BiocFileCache/73cc5931d8b1_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-05-24 06:30:54.787223 loading file /github/home/.cache/R/BiocFileCache/d401e78709e_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 16b19623..0314d5e3 100644
--- a/reference/cluster_export.html
+++ b/reference/cluster_export.html
@@ -134,7 +134,7 @@ 
Examples

     cluster_export(spe, "spatialLIBD")
     cluster_export(spe, "GraphBased")
 }
-#> 2024-05-24 05:48:20.629714 loading file /github/home/.cache/R/BiocFileCache/73cc5931d8b1_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-05-24 06:31:09.85279 loading file /github/home/.cache/R/BiocFileCache/d401e78709e_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 70791b3e..5efc14df 100644
--- a/reference/cluster_import.html
+++ b/reference/cluster_import.html
@@ -137,11 +137,11 @@ 
Examples

     ## Re-import them
     colData(cluster_import(spe))
 }
-#> 2024-05-24 05:48:35.274884 loading file /github/home/.cache/R/BiocFileCache/73cc5931d8b1_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-05-24 06:31:24.282307 loading file /github/home/.cache/R/BiocFileCache/d401e78709e_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
 #> Overwriting 'spe$key'. Set 'overwrite = FALSE' if you do not want to overwrite it.
-#> Warning: '/tmp/Rtmp7tBTHQ/exported_clusters/spatialLIBD' already exists
+#> Warning: '/tmp/RtmpQX6o9B/exported_clusters/spatialLIBD' already exists
 #> Overwriting 'spe$key'. Set 'overwrite = FALSE' if you do not want to overwrite it.
-#> Warning: '/tmp/Rtmp7tBTHQ/exported_clusters/GraphBased' already exists
+#> Warning: '/tmp/RtmpQX6o9B/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 e081beab..5519970a 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")
-#> 2024-05-24 05:48:51.134351 loading file /github/home/.cache/R/BiocFileCache/68fe3214d83_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-05-24 06:31:39.567145 loading file /github/home/.cache/R/BiocFileCache/272335c9fe4_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 dbc92546..286e6f50 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")
 }
-#> 2024-05-24 05:48:53.191024 loading file /github/home/.cache/R/BiocFileCache/73cc5931d8b1_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-05-24 06:31:41.17375 loading file /github/home/.cache/R/BiocFileCache/d401e78709e_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 1e6bc03d..bf36d8fe 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")
 }
-#> 2024-05-24 05:49:08.483289 loading file /github/home/.cache/R/BiocFileCache/68fe5f60223e_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
+#> 2024-05-24 06:31:55.814905 loading file /github/home/.cache/R/BiocFileCache/2723d218943_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 6d4ba0f2..43846ba4 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")
 }
-#> 2024-05-24 05:49:09.971242 loading file /github/home/.cache/R/BiocFileCache/68fe5f60223e_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
+#> 2024-05-24 06:31:57.168311 loading file /github/home/.cache/R/BiocFileCache/2723d218943_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 d8259785..db6da217 100644
--- a/reference/geom_spatial.html
+++ b/reference/geom_spatial.html
@@ -175,7 +175,7 @@ 
Examples

     ## Clean up
     rm(spe_sub)
 }
-#> 2024-05-24 05:49:12.317664 loading file /github/home/.cache/R/BiocFileCache/73cc5931d8b1_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-05-24 06:31:59.036277 loading file /github/home/.cache/R/BiocFileCache/d401e78709e_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
diff --git a/reference/get_colors.html b/reference/get_colors.html index c7fac23b..20813d9e 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")
-#> 2024-05-24 05:49:28.10774 loading file /github/home/.cache/R/BiocFileCache/68fe3214d83_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-05-24 06:32:14.236607 loading file /github/home/.cache/R/BiocFileCache/272335c9fe4_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 63da8db4..9157c862 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)
 }
-#> 2024-05-24 05:49:29.373656 loading file /github/home/.cache/R/BiocFileCache/73cc5931d8b1_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-05-24 06:32:15.433287 loading file /github/home/.cache/R/BiocFileCache/d401e78709e_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
diff --git a/reference/img_update.html b/reference/img_update.html index 6b9cceca..76c61e13 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)) } -#> 2024-05-24 05:49:44.91847 loading file /github/home/.cache/R/BiocFileCache/73cc5931d8b1_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-05-24 06:32:30.927966 loading file /github/home/.cache/R/BiocFileCache/d401e78709e_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 0d8039e9..3c7f7575 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)) } -#> 2024-05-24 05:49:59.062114 loading file /github/home/.cache/R/BiocFileCache/73cc5931d8b1_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-05-24 06:32:44.879917 loading file /github/home/.cache/R/BiocFileCache/d401e78709e_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 32a06ff4..0fe510ed 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") } -#> 2024-05-24 05:50:15.70748 loading file /github/home/.cache/R/BiocFileCache/68fe5f60223e_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1 +#> 2024-05-24 06:33:01.260983 loading file /github/home/.cache/R/BiocFileCache/2723d218943_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1 if (!exists("sce_layer")) sce_layer <- fetch_data(type = "sce_layer") -#> 2024-05-24 05:50:16.58345 loading file /github/home/.cache/R/BiocFileCache/68fe3214d83_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-05-24 06:33:02.130377 loading file /github/home/.cache/R/BiocFileCache/272335c9fe4_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 57b76426..2381e54c 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") } -#> 2024-05-24 05:50:20.228355 loading file /github/home/.cache/R/BiocFileCache/68fe5f60223e_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1 +#> 2024-05-24 06:33:05.460015 loading file /github/home/.cache/R/BiocFileCache/2723d218943_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 45b4f1e9..e4172542 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") } -#> 2024-05-24 05:50:22.252262 loading file /github/home/.cache/R/BiocFileCache/68fe5f60223e_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1 +#> 2024-05-24 06:33:07.342236 loading file /github/home/.cache/R/BiocFileCache/2723d218943_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 20c68c0d..10599ebd 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) -#> 2024-05-24 05:50:24.509212 make pseudobulk object -#> 2024-05-24 05:50:24.751012 drop lowly expressed genes -#> 2024-05-24 05:50:24.824789 normalize expression +#> 2024-05-24 06:33:09.492637 make pseudobulk object +#> 2024-05-24 06:33:09.717641 drop lowly expressed genes +#> 2024-05-24 06:33:09.785735 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") -#> 2024-05-24 05:50:24.904964 create model matrix +#> 2024-05-24 06:33:09.862063 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) -#> 2024-05-24 05:50:24.918173 run duplicateCorrelation() -#> 2024-05-24 05:50:26.22293 The estimated correlation is: -0.0187869166526901 +#> 2024-05-24 06:33:09.876051 run duplicateCorrelation() +#> 2024-05-24 06:33:11.16522 The estimated correlation is: -0.0187869166526901 diff --git a/reference/registration_model.html b/reference/registration_model.html index f04e8cc4..29bebcbc 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) -#> 2024-05-24 05:50:26.673458 make pseudobulk object -#> 2024-05-24 05:50:26.863051 drop lowly expressed genes -#> 2024-05-24 05:50:26.918813 normalize expression +#> 2024-05-24 06:33:11.596051 make pseudobulk object +#> 2024-05-24 06:33:11.777462 drop lowly expressed genes +#> 2024-05-24 06:33:11.829713 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") -#> 2024-05-24 05:50:26.994581 create model matrix +#> 2024-05-24 06:33:11.901191 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 8017ac3c..b8311d16 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) -#> 2024-05-24 05:50:27.465287 make pseudobulk object -#> 2024-05-24 05:50:27.618567 drop lowly expressed genes -#> 2024-05-24 05:50:27.672559 normalize expression +#> 2024-05-24 06:33:12.342844 make pseudobulk object +#> 2024-05-24 06:33:12.48958 drop lowly expressed genes +#> 2024-05-24 06:33:12.54108 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 80f6a429..20c56458 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) -#> 2024-05-24 05:50:28.292759 make pseudobulk object -#> 2024-05-24 05:50:28.44509 drop lowly expressed genes -#> 2024-05-24 05:50:28.498695 normalize expression +#> 2024-05-24 06:33:13.153337 make pseudobulk object +#> 2024-05-24 06:33:13.304993 drop lowly expressed genes +#> 2024-05-24 06:33:13.357234 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") -#> 2024-05-24 05:50:28.57253 create model matrix +#> 2024-05-24 06:33:13.428298 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) -#> 2024-05-24 05:50:28.583899 run duplicateCorrelation() -#> 2024-05-24 05:50:29.89694 The estimated correlation is: -0.0187869166526901 +#> 2024-05-24 06:33:13.438893 run duplicateCorrelation() +#> 2024-05-24 06:33:14.715774 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" ) -#> 2024-05-24 05:50:29.909689 computing F-statistics +#> 2024-05-24 06:33:14.727552 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" ) -#> 2024-05-24 05:50:29.971951 computing F-statistics +#> 2024-05-24 06:33:14.812758 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" ) -#> 2024-05-24 05:50:30.020874 computing F-statistics +#> 2024-05-24 06:33:14.860679 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 0a6d6ba2..9c83db9f 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) -#> 2024-05-24 05:50:30.592059 make pseudobulk object -#> 2024-05-24 05:50:30.743506 drop lowly expressed genes -#> 2024-05-24 05:50:30.797222 normalize expression +#> 2024-05-24 06:33:15.413919 make pseudobulk object +#> 2024-05-24 06:33:15.560752 drop lowly expressed genes +#> 2024-05-24 06:33:15.612442 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") -#> 2024-05-24 05:50:30.869925 create model matrix +#> 2024-05-24 06:33:15.685704 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) -#> 2024-05-24 05:50:30.881151 run duplicateCorrelation() -#> 2024-05-24 05:50:32.181287 The estimated correlation is: -0.0187869166526901 +#> 2024-05-24 06:33:15.69641 run duplicateCorrelation() +#> 2024-05-24 06:33:16.977484 The estimated correlation is: -0.0187869166526901 results_enrichment <- registration_stats_enrichment(sce_pseudo, block_cor, "age", gene_ensembl = "ensembl", gene_name = "gene_name" ) -#> 2024-05-24 05:50:32.184985 computing enrichment statistics -#> 2024-05-24 05:50:32.302896 extract and reformat enrichment results +#> 2024-05-24 06:33:16.980926 computing enrichment statistics +#> 2024-05-24 06:33:17.093063 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" ) -#> 2024-05-24 05:50:32.33577 computing enrichment statistics -#> 2024-05-24 05:50:32.43821 extract and reformat enrichment results +#> 2024-05-24 06:33:17.12484 computing enrichment statistics +#> 2024-05-24 06:33:17.224913 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 10be5a71..49d84646 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) -#> 2024-05-24 05:50:32.928865 make pseudobulk object -#> 2024-05-24 05:50:33.079768 drop lowly expressed genes -#> 2024-05-24 05:50:33.1335 normalize expression +#> 2024-05-24 06:33:17.699434 make pseudobulk object +#> 2024-05-24 06:33:17.847348 drop lowly expressed genes +#> 2024-05-24 06:33:17.899635 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") -#> 2024-05-24 05:50:33.206179 create model matrix +#> 2024-05-24 06:33:17.970375 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) -#> 2024-05-24 05:50:33.217476 run duplicateCorrelation() -#> 2024-05-24 05:50:34.516801 The estimated correlation is: -0.0187869166526901 +#> 2024-05-24 06:33:17.981199 run duplicateCorrelation() +#> 2024-05-24 06:33:19.275373 The estimated correlation is: -0.0187869166526901 results_pairwise <- registration_stats_pairwise(sce_pseudo, registration_mod, block_cor, gene_ensembl = "ensembl", gene_name = "gene_name" ) -#> 2024-05-24 05:50:34.518799 running the baseline pairwise model -#> 2024-05-24 05:50:34.535402 computing pairwise statistics +#> 2024-05-24 06:33:19.277411 running the baseline pairwise model +#> 2024-05-24 06:33:19.29375 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" ) -#> 2024-05-24 05:50:34.599254 running the baseline pairwise model -#> 2024-05-24 05:50:34.616195 computing pairwise statistics +#> 2024-05-24 06:33:19.357572 running the baseline pairwise model +#> 2024-05-24 06:33:19.374381 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 a81276af..7f337310 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" ) -#> 2024-05-24 05:50:35.141741 make pseudobulk object -#> 2024-05-24 05:50:35.322581 dropping 9 pseudo-bulked samples that are below 'min_ncells'. -#> 2024-05-24 05:50:35.343219 drop lowly expressed genes -#> 2024-05-24 05:50:35.396023 normalize expression -#> 2024-05-24 05:50:35.452259 create model matrix -#> 2024-05-24 05:50:35.462711 run duplicateCorrelation() -#> 2024-05-24 05:50:37.881039 The estimated correlation is: -0.0783081238514532 -#> 2024-05-24 05:50:37.883224 computing enrichment statistics -#> 2024-05-24 05:50:37.997214 extract and reformat enrichment results -#> 2024-05-24 05:50:38.022151 running the baseline pairwise model -#> 2024-05-24 05:50:38.039508 computing pairwise statistics -#> 2024-05-24 05:50:38.111841 computing F-statistics +#> 2024-05-24 06:33:19.889828 make pseudobulk object +#> 2024-05-24 06:33:20.063577 dropping 9 pseudo-bulked samples that are below 'min_ncells'. +#> 2024-05-24 06:33:20.083559 drop lowly expressed genes +#> 2024-05-24 06:33:20.134552 normalize expression +#> 2024-05-24 06:33:20.189356 create model matrix +#> 2024-05-24 06:33:20.199538 run duplicateCorrelation() +#> 2024-05-24 06:33:22.589525 The estimated correlation is: -0.0783081238514532 +#> 2024-05-24 06:33:22.591635 computing enrichment statistics +#> 2024-05-24 06:33:22.702667 extract and reformat enrichment results +#> 2024-05-24 06:33:22.727031 running the baseline pairwise model +#> 2024-05-24 06:33:22.744089 computing pairwise statistics +#> 2024-05-24 06:33:22.815567 computing F-statistics diff --git a/reference/sce_to_spe.html b/reference/sce_to_spe.html index 8f6d0752..59baa144 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) } -#> 2024-05-24 05:50:40.40029 loading file /github/home/.cache/R/BiocFileCache/73cc5931d8b1_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-05-24 06:33:24.996505 loading file /github/home/.cache/R/BiocFileCache/d401e78709e_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 e9387ed4..c3314ce4 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") } -#> 2024-05-24 05:50:53.360073 loading file /github/home/.cache/R/BiocFileCache/68fe5f60223e_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1 +#> 2024-05-24 06:33:37.791004 loading file /github/home/.cache/R/BiocFileCache/2723d218943_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1 if (!exists("sce_layer")) sce_layer <- fetch_data(type = "sce_layer") -#> 2024-05-24 05:50:54.565986 loading file /github/home/.cache/R/BiocFileCache/68fe3214d83_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-05-24 06:33:38.882315 loading file /github/home/.cache/R/BiocFileCache/272335c9fe4_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 3996dd22..6205e7c0 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") } -#> 2024-05-24 05:50:58.36718 loading file /github/home/.cache/R/BiocFileCache/68fe5f60223e_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1 +#> 2024-05-24 06:33:42.675083 loading file /github/home/.cache/R/BiocFileCache/2723d218943_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1 if (!exists("sce_layer")) sce_layer <- fetch_data(type = "sce_layer") -#> 2024-05-24 05:50:59.452519 loading file /github/home/.cache/R/BiocFileCache/68fe3214d83_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-05-24 06:33:43.573064 loading file /github/home/.cache/R/BiocFileCache/272335c9fe4_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 e0de4a8e..a4ff208d 100644 --- a/reference/vis_clus.html +++ b/reference/vis_clus.html @@ -232,7 +232,7 @@

Examples

) print(p4) } -#> 2024-05-24 05:51:02.857355 loading file /github/home/.cache/R/BiocFileCache/73cc5931d8b1_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-05-24 06:33:46.755551 loading file /github/home/.cache/R/BiocFileCache/d401e78709e_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 a6d3516c..07ef5673 100644 --- a/reference/vis_clus_p.html +++ b/reference/vis_clus_p.html @@ -202,7 +202,7 @@

Examples

## Clean up rm(spe_sub) } -#> 2024-05-24 05:51:23.020115 loading file /github/home/.cache/R/BiocFileCache/73cc5931d8b1_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-05-24 06:34:06.16246 loading file /github/home/.cache/R/BiocFileCache/d401e78709e_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 diff --git a/reference/vis_gene.html b/reference/vis_gene.html index 28d8f01c..2310a0ba 100644 --- a/reference/vis_gene.html +++ b/reference/vis_gene.html @@ -331,7 +331,7 @@

Examples

) print(p8) } -#> 2024-05-24 05:51:37.87177 loading file /github/home/.cache/R/BiocFileCache/73cc5931d8b1_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-05-24 06:34:21.777627 loading file /github/home/.cache/R/BiocFileCache/d401e78709e_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 4e864074..0af2eea4 100644 --- a/reference/vis_gene_p.html +++ b/reference/vis_gene_p.html @@ -220,7 +220,7 @@

Examples

## Clean up rm(spe_sub) } -#> 2024-05-24 05:52:03.754183 loading file /github/home/.cache/R/BiocFileCache/73cc5931d8b1_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-05-24 06:34:47.45786 loading file /github/home/.cache/R/BiocFileCache/d401e78709e_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 8a26ae24..0fd03440 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) } -#> 2024-05-24 05:52:18.567921 loading file /github/home/.cache/R/BiocFileCache/73cc5931d8b1_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-05-24 06:35:02.328426 loading file /github/home/.cache/R/BiocFileCache/d401e78709e_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 083c861d..ed33831a 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) } -#> 2024-05-24 05:52:34.845136 loading file /github/home/.cache/R/BiocFileCache/73cc5931d8b1_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-05-24 06:35:18.741817 loading file /github/home/.cache/R/BiocFileCache/d401e78709e_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1