From 233aeab651cc68e6730e86b11a7e01a9ddd20934 Mon Sep 17 00:00:00 2001 From: lcolladotor Date: Thu, 12 Dec 2024 20:20:00 +0000 Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20LieberIn?= =?UTF-8?q?stitute/spatialLIBD@eebcdad8505266107562063ad2326faa26fa6d07=20?= =?UTF-8?q?=F0=9F=9A=80?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- 404.html | 2 +- CODE_OF_CONDUCT.html | 2 +- CONTRIBUTING.html | 2 +- SUPPORT.html | 2 +- articles/TenX_data_download.html | 22 ++++++------ articles/guide_to_spatial_registration.html | 34 +++++++++---------- articles/index.html | 2 +- articles/multi_gene_plots.html | 12 +++---- articles/spatialLIBD.html | 16 ++++----- authors.html | 2 +- index.html | 2 +- news/index.html | 7 +++- pkgdown.yml | 2 +- reference/add10xVisiumAnalysis.html | 2 +- reference/add_images.html | 28 +++++++-------- reference/add_key.html | 4 +-- reference/add_qc_metrics.html | 4 +-- reference/annotate_registered_clusters.html | 4 +-- reference/check_modeling_results.html | 4 +-- reference/check_sce.html | 4 +-- reference/check_sce_layer.html | 4 +-- reference/check_spe.html | 4 +-- reference/cluster_export.html | 4 +-- reference/cluster_import.html | 8 ++--- reference/enough_ram.html | 2 +- reference/fetch_data.html | 4 +-- reference/frame_limits.html | 4 +-- reference/gene_set_enrichment.html | 4 +-- reference/gene_set_enrichment_plot.html | 4 +-- reference/geom_spatial.html | 4 +-- reference/get_colors.html | 4 +-- reference/img_edit.html | 4 +-- reference/img_update.html | 4 +-- reference/img_update_all.html | 4 +-- reference/index.html | 2 +- reference/layer_boxplot.html | 6 ++-- reference/layer_matrix_plot.html | 2 +- reference/layer_stat_cor.html | 4 +-- reference/layer_stat_cor_plot.html | 6 ++-- reference/libd_layer_colors.html | 2 +- reference/locate_images.html | 2 +- reference/multi_gene_pca.html | 2 +- reference/multi_gene_sparsity.html | 2 +- reference/multi_gene_z_score.html | 2 +- reference/prep_stitched_data.html | 2 +- reference/read10xVisiumAnalysis.html | 2 +- reference/read10xVisiumWrapper.html | 2 +- reference/registration_block_cor.html | 14 ++++---- reference/registration_model.html | 10 +++--- reference/registration_pseudobulk.html | 12 ++++--- reference/registration_stats_anova.html | 20 +++++------ reference/registration_stats_enrichment.html | 22 ++++++------ reference/registration_stats_pairwise.html | 22 ++++++------ reference/registration_wrapper.html | 30 ++++++++-------- reference/run_app.html | 2 +- reference/sce_to_spe.html | 4 +-- reference/sig_genes_extract.html | 6 ++-- reference/sig_genes_extract_all.html | 6 ++-- reference/sort_clusters.html | 2 +- reference/spatialLIBD-package.html | 2 +- ..._Human_DLPFC_snRNAseq_Nguyen_topLayer.html | 2 +- reference/vis_clus.html | 4 +-- reference/vis_clus_p.html | 4 +-- reference/vis_gene.html | 4 +-- reference/vis_gene_p.html | 4 +-- reference/vis_grid_clus.html | 4 +-- reference/vis_grid_gene.html | 4 +-- 67 files changed, 219 insertions(+), 210 deletions(-) diff --git a/404.html b/404.html index 03190016..9e63ee19 100644 --- a/404.html +++ b/404.html @@ -40,7 +40,7 @@ spatialLIBD - 1.19.1 + 1.19.2 diff --git a/CODE_OF_CONDUCT.html b/CODE_OF_CONDUCT.html index 8d1482ca..6fe03f99 100644 --- a/CODE_OF_CONDUCT.html +++ b/CODE_OF_CONDUCT.html @@ -17,7 +17,7 @@ spatialLIBD - 1.19.1 + 1.19.2 diff --git a/CONTRIBUTING.html b/CONTRIBUTING.html index 8d7005ac..259f4a54 100644 --- a/CONTRIBUTING.html +++ b/CONTRIBUTING.html @@ -17,7 +17,7 @@ spatialLIBD - 1.19.1 + 1.19.2 diff --git a/SUPPORT.html b/SUPPORT.html index bb9bc0e3..2f46428c 100644 --- a/SUPPORT.html +++ b/SUPPORT.html @@ -17,7 +17,7 @@ spatialLIBD - 1.19.1 + 1.19.2 diff --git a/articles/TenX_data_download.html b/articles/TenX_data_download.html index e09a2cf4..4f03684e 100644 --- a/articles/TenX_data_download.html +++ b/articles/TenX_data_download.html @@ -39,7 +39,7 @@ spatialLIBD - 1.19.1 + 1.19.2 @@ -532,7 +532,7 @@

From Gencode## Show the GTF cache location gtf_cache #> BFC4 -#> "/github/home/.cache/R/BiocFileCache/5c6a7dbe81_gencode.v32.annotation.gtf.gz" +#> "/github/home/.cache/R/BiocFileCache/5c71d57fde_gencode.v32.annotation.gtf.gz" ## Import into R (takes ~1 min) gtf <- rtracklayer::import(gtf_cache) @@ -818,11 +818,11 @@

Wrapper functions= c("lowres", "hires", "detected", "aligned"), load = TRUE, reference_gtf = gtf_cache ) -#> 2024-12-12 20:13:56.419903 SpatialExperiment::read10xVisium: reading basic data from SpaceRanger -#> 2024-12-12 20:14:06.59609 read10xVisiumAnalysis: reading analysis output from SpaceRanger -#> 2024-12-12 20:14:07.647298 add10xVisiumAnalysis: adding analysis output from SpaceRanger -#> 2024-12-12 20:14:07.801939 rtracklayer::import: reading the reference GTF file -#> 2024-12-12 20:14:32.428294 adding gene information to the SPE object +#> 2024-12-12 20:19:09.681751 SpatialExperiment::read10xVisium: reading basic data from SpaceRanger +#> 2024-12-12 20:19:19.963575 read10xVisiumAnalysis: reading analysis output from SpaceRanger +#> 2024-12-12 20:19:21.059095 add10xVisiumAnalysis: adding analysis output from SpaceRanger +#> 2024-12-12 20:19:21.207331 rtracklayer::import: reading the reference GTF file +#> 2024-12-12 20:19:45.832527 adding gene information to the SPE object #> Warning: Gene IDs did not match. This typically happens when you are not using #> the same GTF file as the one that was used by SpaceRanger. For example, one #> file uses GENCODE IDs and the other one ENSEMBL IDs. read10xVisiumWrapper() @@ -830,7 +830,7 @@

Wrapper functions#> Warning: Dropping 29 out of 36601 genes for which we don't have information on #> the reference GTF file. This typically happens when you are not using the same #> GTF file as the one that was used by SpaceRanger. -#> 2024-12-12 20:14:33.863742 adding information used by spatialLIBD +#> 2024-12-12 20:19:47.339986 adding information used by spatialLIBD 
 ## Run our shiny app
 if (interactive()) {
@@ -1114,9 +1114,9 @@ 
Reproducibilitylibrary("knitr")
 knit("TenX_data_download.Rmd", tangle = TRUE)

Date the vignette was generated.

-
#> [1] "2024-12-12 20:14:34 UTC"
+
#> [1] "2024-12-12 20:19:48 UTC"

Wallclock time spent generating the vignette.

-
#> Time difference of 1.646 mins
+
#> Time difference of 1.664 mins

R session information.

#> ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
 #>  setting  value
@@ -1287,7 +1287,7 @@ 
Reproducibility#>  SparseArray            1.6.0     2024-10-29 [1] Bioconductor 3.20 (R 4.4.2)
 #>  sparseMatrixStats      1.18.0    2024-10-29 [1] Bioconductor 3.20 (R 4.4.2)
 #>  SpatialExperiment    * 1.16.0    2024-10-29 [1] Bioconductor 3.20 (R 4.4.2)
-#>  spatialLIBD          * 1.19.1    2024-12-12 [1] Bioconductor
+#>  spatialLIBD          * 1.19.2    2024-12-12 [1] Bioconductor
 #>  statmod                1.5.0     2023-01-06 [1] RSPM (R 4.4.0)
 #>  stringi                1.8.4     2024-05-06 [2] RSPM (R 4.4.0)
 #>  stringr                1.5.1     2023-11-14 [2] RSPM (R 4.4.0)
diff --git a/articles/guide_to_spatial_registration.html b/articles/guide_to_spatial_registration.html
index 038e26f2..1c8e6ed5 100644
--- a/articles/guide_to_spatial_registration.html
+++ b/articles/guide_to_spatial_registration.html
@@ -39,7 +39,7 @@
       
       
         spatialLIBD
-        1.19.1
+        1.19.2
       
     
 
@@ -288,7 +288,7 @@ 
Spatial Reference
 ## get reference layer enrichment statistics
 layer_modeling_results <- fetch_data(type = "modeling_results")
-#> 2024-12-12 20:11:00.268595 loading file /github/home/.cache/R/BiocFileCache/5c643ff6574_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
+#> 2024-12-12 20:16:14.237373 loading file /github/home/.cache/R/BiocFileCache/5c73806c84a_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
 
 layer_modeling_results$enrichment[1:5, 1:5]
 #>    t_stat_WM t_stat_Layer1 t_stat_Layer2 t_stat_Layer3 t_stat_Layer4
@@ -391,18 +391,18 @@ 
Get Enrichment statistics
     gene_ensembl = "gene_id",
     gene_name = "gene_name"
 )
-#> 2024-12-12 20:11:08.137818 make pseudobulk object
-#> 2024-12-12 20:11:09.784836 dropping 13 pseudo-bulked samples that are below 'min_ncells'.
-#> 2024-12-12 20:11:09.829241 drop lowly expressed genes
-#> 2024-12-12 20:11:09.986814 normalize expression
-#> 2024-12-12 20:11:11.493804 create model matrix
-#> 2024-12-12 20:11:11.517093 run duplicateCorrelation()
-#> 2024-12-12 20:11:24.698387 The estimated correlation is: 0.138734774807097
-#> 2024-12-12 20:11:24.7013 computing enrichment statistics
-#> 2024-12-12 20:11:25.915521 extract and reformat enrichment results
-#> 2024-12-12 20:11:25.971312 running the baseline pairwise model
-#> 2024-12-12 20:11:26.125053 computing pairwise statistics
-#> 2024-12-12 20:11:28.250693 computing F-statistics

+#> 2024-12-12 20:16:22.448405 make pseudobulk object
+#> 2024-12-12 20:16:24.149791 dropping 13 pseudo-bulked samples that are below 'min_ncells'.
+#> 2024-12-12 20:16:24.194799 drop lowly expressed genes
+#> 2024-12-12 20:16:24.349038 normalize expression
+#> 2024-12-12 20:16:25.890173 create model matrix
+#> 2024-12-12 20:16:25.913575 run duplicateCorrelation()
+#> 2024-12-12 20:16:38.936856 The estimated correlation is: 0.138734774807097
+#> 2024-12-12 20:16:38.939658 computing enrichment statistics
+#> 2024-12-12 20:16:40.187687 extract and reformat enrichment results
+#> 2024-12-12 20:16:40.245241 running the baseline pairwise model
+#> 2024-12-12 20:16:40.39009 computing pairwise statistics
+#> 2024-12-12 20:16:42.593259 computing F-statistics

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

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

Date the vignette was generated.

-
#> [1] "2024-12-12 20:11:31 UTC"
+
#> [1] "2024-12-12 20:16:45 UTC"

Wallclock time spent generating the vignette.

-
#> Time difference of 43.561 secs
+
#> Time difference of 43.786 secs

R session information.

#> ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
 #>  setting  value
@@ -737,7 +737,7 @@ 
Reproducibility#>  spam                   2.11-0    2024-10-03 [1] RSPM (R 4.4.0)
 #>  SparseArray            1.6.0     2024-10-29 [1] Bioconductor 3.20 (R 4.4.2)
 #>  SpatialExperiment    * 1.16.0    2024-10-29 [1] Bioconductor 3.20 (R 4.4.2)
-#>  spatialLIBD          * 1.19.1    2024-12-12 [1] Bioconductor
+#>  spatialLIBD          * 1.19.2    2024-12-12 [1] Bioconductor
 #>  statmod                1.5.0     2023-01-06 [1] RSPM (R 4.4.0)
 #>  stringi                1.8.4     2024-05-06 [2] RSPM (R 4.4.0)
 #>  stringr                1.5.1     2023-11-14 [2] RSPM (R 4.4.0)
diff --git a/articles/index.html b/articles/index.html
index 6619dc98..135201eb 100644
--- a/articles/index.html
+++ b/articles/index.html
@@ -17,7 +17,7 @@
       
       
         spatialLIBD
-        1.19.1
+        1.19.2
       
     
 
diff --git a/articles/multi_gene_plots.html b/articles/multi_gene_plots.html
index 22bfbb3c..fb27358f 100644
--- a/articles/multi_gene_plots.html
+++ b/articles/multi_gene_plots.html
@@ -39,7 +39,7 @@
       
       
         spatialLIBD
-        1.19.1
+        1.19.2
       
     
 
@@ -195,9 +195,9 @@ 
Plotting One Gene
 modeling_results <- fetch_data(type = "modeling_results")
-#> 2024-12-12 20:11:55.351142 loading file /github/home/.cache/R/BiocFileCache/5c643ff6574_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
+#> 2024-12-12 20:17:08.833029 loading file /github/home/.cache/R/BiocFileCache/5c73806c84a_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
 sce_layer <- fetch_data(type = "sce_layer")
-#> 2024-12-12 20:11:56.728664 loading file /github/home/.cache/R/BiocFileCache/5c61202c143_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-12-12 20:17:09.724514 loading file /github/home/.cache/R/BiocFileCache/5c77b6ee4a2_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
 sig_genes <- sig_genes_extract_all(
     n = 400,
     modeling_results = modeling_results,
@@ -421,9 +421,9 @@ 
Reproducibilitylibrary("knitr")
 knit("multi_gene_plots.Rmd", tangle = TRUE)

 
Date the vignette was generated.

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

+
#> [1] "2024-12-12 20:17:25 UTC"

 
Wallclock time spent generating the vignette.

-
#> Time difference of 37.141 secs

+
#> Time difference of 36.102 secs

 
R session information.

 
#> ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
 #>  setting  value
@@ -581,7 +581,7 @@ 
Reproducibility#>  spam                   2.11-0    2024-10-03 [1] RSPM (R 4.4.0)
 #>  SparseArray            1.6.0     2024-10-29 [1] Bioconductor 3.20 (R 4.4.2)
 #>  SpatialExperiment    * 1.16.0    2024-10-29 [1] Bioconductor 3.20 (R 4.4.2)
-#>  spatialLIBD          * 1.19.1    2024-12-12 [1] Bioconductor
+#>  spatialLIBD          * 1.19.2    2024-12-12 [1] Bioconductor
 #>  statmod                1.5.0     2023-01-06 [1] RSPM (R 4.4.0)
 #>  stringi                1.8.4     2024-05-06 [2] RSPM (R 4.4.0)
 #>  stringr                1.5.1     2023-11-14 [2] RSPM (R 4.4.0)
diff --git a/articles/spatialLIBD.html b/articles/spatialLIBD.html
index 2750a815..e22b6926 100644
--- a/articles/spatialLIBD.html
+++ b/articles/spatialLIBD.html
@@ -39,7 +39,7 @@
       
       
         spatialLIBD
-        1.19.1
+        1.19.2
       
     
 
@@ -414,7 +414,7 @@ 
Downloading the data with s
 
 ## Download the small example sce data
 sce <- fetch_data(type = "sce_example", eh = ehub)
-#> 2024-12-12 20:12:28.826377 loading file /github/home/.cache/R/BiocFileCache/5c66f42346d_sce_sub_for_vignette.Rdata%3Fdl%3D1
+#> 2024-12-12 20:17:41.230595 loading file /github/home/.cache/R/BiocFileCache/5c772064dd8_sce_sub_for_vignette.Rdata%3Fdl%3D1
 
 ## Convert to a SpatialExperiment object
 spe <- sce_to_spe(sce)
@@ -426,9 +426,9 @@ 
Downloading the data with s
 
 ## Query ExperimentHub and download the data
 if (!exists("sce_layer")) sce_layer <- fetch_data(type = "sce_layer", eh = ehub)
-#> 2024-12-12 20:12:33.031734 loading file /github/home/.cache/R/BiocFileCache/5c61202c143_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-12-12 20:17:45.41416 loading file /github/home/.cache/R/BiocFileCache/5c77b6ee4a2_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
 modeling_results <- fetch_data("modeling_results", eh = ehub)
-#> 2024-12-12 20:12:33.472108 loading file /github/home/.cache/R/BiocFileCache/5c643ff6574_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1

+#> 2024-12-12 20:17:45.850986 loading file /github/home/.cache/R/BiocFileCache/5c73806c84a_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1

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

 
@@ -501,7 +501,7 @@ 
Downloading the data with s
         )
 )
 #>    user  system elapsed 
-#>   9.464   0.376   9.859
+#>   9.493   0.440   9.952
 
 ## Explore the result
 class(sig_genes)
@@ -1383,9 +1383,9 @@ 
Reproducibilitylibrary("knitr")
 knit("spatialLIBD.Rmd", tangle = TRUE)

 
Date the vignette was generated.

-
#> [1] "2024-12-12 20:12:51 UTC"

+
#> [1] "2024-12-12 20:18:04 UTC"

 
Wallclock time spent generating the vignette.

-
#> Time difference of 35.593 secs

+
#> Time difference of 35.251 secs

 
R session information.

 
#> ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
 #>  setting  value
@@ -1544,7 +1544,7 @@ 
Reproducibility#>  spam                   2.11-0    2024-10-03 [1] RSPM (R 4.4.0)
 #>  SparseArray            1.6.0     2024-10-29 [1] Bioconductor 3.20 (R 4.4.2)
 #>  SpatialExperiment    * 1.16.0    2024-10-29 [1] Bioconductor 3.20 (R 4.4.2)
-#>  spatialLIBD          * 1.19.1    2024-12-12 [1] Bioconductor
+#>  spatialLIBD          * 1.19.2    2024-12-12 [1] Bioconductor
 #>  statmod                1.5.0     2023-01-06 [1] RSPM (R 4.4.0)
 #>  stringi                1.8.4     2024-05-06 [2] RSPM (R 4.4.0)
 #>  stringr                1.5.1     2023-11-14 [2] RSPM (R 4.4.0)
diff --git a/authors.html b/authors.html
index b652a12d..a82f81ea 100644
--- a/authors.html
+++ b/authors.html
@@ -17,7 +17,7 @@
       
       
         spatialLIBD
-        1.19.1
+        1.19.2
       
     
 
diff --git a/index.html b/index.html
index cbe5e0cd..35f54314 100644
--- a/index.html
+++ b/index.html
@@ -41,7 +41,7 @@
       
       
         spatialLIBD
-        1.19.1
+        1.19.2
       
     
 
diff --git a/news/index.html b/news/index.html
index 20d6c300..0c83d694 100644
--- a/news/index.html
+++ b/news/index.html
@@ -17,7 +17,7 @@
       
       
         spatialLIBD
-        1.19.1
+        1.19.2
       
     
 
@@ -66,6 +66,11 @@ 
Changelog 

       Source: NEWS.md
     
 
+    

+
spatialLIBD 1.19.2

+
BUG FIXES

+

     

 
spatialLIBD 1.19.1

 
NEW FEATURES

diff --git a/pkgdown.yml b/pkgdown.yml
index 53203f19..e5e3e846 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -6,4 +6,4 @@ articles:
   multi_gene_plots: multi_gene_plots.html
   spatialLIBD: spatialLIBD.html
   TenX_data_download: TenX_data_download.html
-last_built: 2024-12-12T20:06Z
+last_built: 2024-12-12T20:11Z
diff --git a/reference/add10xVisiumAnalysis.html b/reference/add10xVisiumAnalysis.html
index 87ffac93..6872b180 100644
--- a/reference/add10xVisiumAnalysis.html
+++ b/reference/add10xVisiumAnalysis.html
@@ -19,7 +19,7 @@
       
       
         spatialLIBD
-        1.19.1
+        1.19.2
       
     

 
diff --git a/reference/add_images.html b/reference/add_images.html
index 295602a5..eab2b896 100644
--- a/reference/add_images.html
+++ b/reference/add_images.html
@@ -25,7 +25,7 @@
       
       
         spatialLIBD
-        1.19.1
+        1.19.2
       
     
 
@@ -165,29 +165,29 @@ 
Examples

         image_paths = c("151507" = "https://spatial-dlpfc.s3.us-east-2.amazonaws.com/images/151507_tissue_lowres_image.png")
     ))
 }
-#> 2024-12-12 20:06:30.875077 loading file /github/home/.cache/R/BiocFileCache/1048142167f7_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
-#> 2024-12-12 20:06:41.543143 adding image for sample 151507
-#> 2024-12-12 20:06:42.863058 adding image for sample 151508
+#> 2024-12-12 20:12:01.22569 loading file /github/home/.cache/R/BiocFileCache/104970f7ab1e_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-12-12 20:12:12.020288 adding image for sample 151507
+#> 2024-12-12 20:12:12.591118 adding image for sample 151508
 #> Warning: No image was found for sample: 151508
-#> 2024-12-12 20:06:42.863794 adding image for sample 151509
+#> 2024-12-12 20:12:12.591867 adding image for sample 151509
 #> Warning: No image was found for sample: 151509
-#> 2024-12-12 20:06:42.864312 adding image for sample 151510
+#> 2024-12-12 20:12:12.592384 adding image for sample 151510
 #> Warning: No image was found for sample: 151510
-#> 2024-12-12 20:06:42.864798 adding image for sample 151669
+#> 2024-12-12 20:12:12.592872 adding image for sample 151669
 #> Warning: No image was found for sample: 151669
-#> 2024-12-12 20:06:42.865274 adding image for sample 151670
+#> 2024-12-12 20:12:12.593351 adding image for sample 151670
 #> Warning: No image was found for sample: 151670
-#> 2024-12-12 20:06:42.865771 adding image for sample 151671
+#> 2024-12-12 20:12:12.593823 adding image for sample 151671
 #> Warning: No image was found for sample: 151671
-#> 2024-12-12 20:06:42.86624 adding image for sample 151672
+#> 2024-12-12 20:12:12.594292 adding image for sample 151672
 #> Warning: No image was found for sample: 151672
-#> 2024-12-12 20:06:42.866706 adding image for sample 151673
+#> 2024-12-12 20:12:12.594766 adding image for sample 151673
 #> Warning: No image was found for sample: 151673
-#> 2024-12-12 20:06:42.867163 adding image for sample 151674
+#> 2024-12-12 20:12:12.59522 adding image for sample 151674
 #> Warning: No image was found for sample: 151674
-#> 2024-12-12 20:06:42.867632 adding image for sample 151675
+#> 2024-12-12 20:12:12.595699 adding image for sample 151675
 #> Warning: No image was found for sample: 151675
-#> 2024-12-12 20:06:42.868106 adding image for sample 151676
+#> 2024-12-12 20:12:12.596159 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 0dc639cd..4899b513 100644
--- a/reference/add_key.html
+++ b/reference/add_key.html
@@ -19,7 +19,7 @@
       
       
         spatialLIBD
-        1.19.1
+        1.19.2
       
     
 
@@ -124,7 +124,7 @@ 
Examples

     spe$key_original <- NULL
     head(spe$key)
 }
-#> 2024-12-12 20:06:45.589277 loading file /github/home/.cache/R/BiocFileCache/1048142167f7_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-12-12 20:12:14.88532 loading file /github/home/.cache/R/BiocFileCache/104970f7ab1e_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
 #> [1] "151507_AAACAACGAATAGTTC-1" "151507_AAACAAGTATCTCCCA-1"
 #> [3] "151507_AAACAATCTACTAGCA-1" "151507_AAACACCAATAACTGC-1"
 #> [5] "151507_AAACAGCTTTCAGAAG-1" "151507_AAACAGGGTCTATATT-1"
diff --git a/reference/add_qc_metrics.html b/reference/add_qc_metrics.html
index 63d9579f..1889e071 100644
--- a/reference/add_qc_metrics.html
+++ b/reference/add_qc_metrics.html
@@ -21,7 +21,7 @@
       
       
         spatialLIBD
-        1.19.1
+        1.19.2
       
     
 
@@ -144,7 +144,7 @@ 
Author

     
Examples

     
## Obtain the necessary data
 spe_pre_qc <- fetch_data("spatialDLPFC_Visium_example_subset")
-#> 2024-12-12 20:06:56.981917 loading file /github/home/.cache/R/BiocFileCache/5c64699e3d1_spatialDLPFC_spe_subset_example.rds%3Fdl%3D1
+#> 2024-12-12 20:12:25.69285 loading file /github/home/.cache/R/BiocFileCache/5c73918b4f0_spatialDLPFC_spe_subset_example.rds%3Fdl%3D1
 
 ## For now, we fake out tissue spots in example data
 spe_qc <- spe_pre_qc
diff --git a/reference/annotate_registered_clusters.html b/reference/annotate_registered_clusters.html
index 51e42c5b..55c45daa 100644
--- a/reference/annotate_registered_clusters.html
+++ b/reference/annotate_registered_clusters.html
@@ -21,7 +21,7 @@
       
       
         spatialLIBD
-        1.19.1
+        1.19.2
       
     

 
@@ -137,7 +137,7 @@ 
Examples

 if (!exists("modeling_results")) {
     modeling_results <- fetch_data(type = "modeling_results")
 }
-#> 2024-12-12 20:07:09.146699 loading file /github/home/.cache/R/BiocFileCache/5c643ff6574_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
+#> 2024-12-12 20:12:37.236166 loading file /github/home/.cache/R/BiocFileCache/5c73806c84a_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 edd4bd31..1728a83c 100644
--- a/reference/check_modeling_results.html
+++ b/reference/check_modeling_results.html
@@ -18,7 +18,7 @@
       
       
         spatialLIBD
-        1.19.1
+        1.19.2
       
     
 
@@ -109,7 +109,7 @@ 
Examples

 if (!exists("modeling_results")) {
     modeling_results <- fetch_data(type = "modeling_results")
 }
-#> 2024-12-12 20:07:10.459215 loading file /github/home/.cache/R/BiocFileCache/5c643ff6574_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
+#> 2024-12-12 20:12:38.247754 loading file /github/home/.cache/R/BiocFileCache/5c73806c84a_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 5709551d..007aeca7 100644
--- a/reference/check_sce.html
+++ b/reference/check_sce.html
@@ -20,7 +20,7 @@
       
       
         spatialLIBD
-        1.19.1
+        1.19.2
       
     
 
@@ -131,7 +131,7 @@ 
Examples

     ## Check the object
     check_sce(sce_example)
 }
-#> 2024-12-12 20:07:11.726206 loading file /github/home/.cache/R/BiocFileCache/5c66f42346d_sce_sub_for_vignette.Rdata%3Fdl%3D1
+#> 2024-12-12 20:12:39.193695 loading file /github/home/.cache/R/BiocFileCache/5c772064dd8_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 75a4aa27..1a3b8e32 100644
--- a/reference/check_sce_layer.html
+++ b/reference/check_sce_layer.html
@@ -18,7 +18,7 @@
       
       
         spatialLIBD
-        1.19.1
+        1.19.2
       
     
 
@@ -112,7 +112,7 @@ 
Examples

 ## Obtain example data from the HumanPilot project
 ## (Maynard, Collado-Torres, et al, 2021)
 if (!exists("sce_layer")) sce_layer <- fetch_data("sce_layer")
-#> 2024-12-12 20:07:14.244422 loading file /github/home/.cache/R/BiocFileCache/5c61202c143_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-12-12 20:12:41.34337 loading file /github/home/.cache/R/BiocFileCache/5c77b6ee4a2_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
 
 ## Check the pseudo-bulked data
 check_sce_layer(sce_layer)
diff --git a/reference/check_spe.html b/reference/check_spe.html
index 6241cb53..d67cc3f5 100644
--- a/reference/check_spe.html
+++ b/reference/check_spe.html
@@ -18,7 +18,7 @@
       
       
         spatialLIBD
-        1.19.1
+        1.19.2
       
     
 
@@ -123,7 +123,7 @@ 
Examples

     ## Check the object
     check_spe(spe)
 }
-#> 2024-12-12 20:07:15.699239 loading file /github/home/.cache/R/BiocFileCache/1048142167f7_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-12-12 20:12:42.438743 loading file /github/home/.cache/R/BiocFileCache/104970f7ab1e_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 a9699fb4..3844caf5 100644
--- a/reference/cluster_export.html
+++ b/reference/cluster_export.html
@@ -21,7 +21,7 @@
       
       
         spatialLIBD
-        1.19.1
+        1.19.2
       
     
 
@@ -134,7 +134,7 @@ 
Examples

     cluster_export(spe, "spatialLIBD")
     cluster_export(spe, "GraphBased")
 }
-#> 2024-12-12 20:07:25.254271 loading file /github/home/.cache/R/BiocFileCache/1048142167f7_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-12-12 20:12:51.69188 loading file /github/home/.cache/R/BiocFileCache/104970f7ab1e_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 42881050..3bd53ea2 100644
--- a/reference/cluster_import.html
+++ b/reference/cluster_import.html
@@ -20,7 +20,7 @@
       
       
         spatialLIBD
-        1.19.1
+        1.19.2
       
     
 
@@ -137,11 +137,11 @@ 
Examples

     ## Re-import them
     colData(cluster_import(spe))
 }
-#> 2024-12-12 20:07:36.741357 loading file /github/home/.cache/R/BiocFileCache/1048142167f7_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-12-12 20:13:02.037251 loading file /github/home/.cache/R/BiocFileCache/104970f7ab1e_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
 #> Overwriting 'spe$key'. Set 'overwrite = FALSE' if you do not want to overwrite it.
-#> Warning: '/tmp/RtmpHefYvC/exported_clusters/spatialLIBD' already exists
+#> Warning: '/tmp/Rtmpzq7cH3/exported_clusters/spatialLIBD' already exists
 #> Overwriting 'spe$key'. Set 'overwrite = FALSE' if you do not want to overwrite it.
-#> Warning: '/tmp/RtmpHefYvC/exported_clusters/GraphBased' already exists
+#> Warning: '/tmp/Rtmpzq7cH3/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/enough_ram.html b/reference/enough_ram.html
index 27f42f20..fd08c505 100644
--- a/reference/enough_ram.html
+++ b/reference/enough_ram.html
@@ -17,7 +17,7 @@
       
       
         spatialLIBD
-        1.19.1
+        1.19.2
       
     
 
diff --git a/reference/fetch_data.html b/reference/fetch_data.html
index 1baa67eb..13997af3 100644
--- a/reference/fetch_data.html
+++ b/reference/fetch_data.html
@@ -25,7 +25,7 @@
       
       
         spatialLIBD
-        1.19.1
+        1.19.2
       
     
 
@@ -166,7 +166,7 @@ 
Examples

 ## Download the SingleCellExperiment object
 ## at the layer-level
 if (!exists("sce_layer")) sce_layer <- fetch_data("sce_layer")
-#> 2024-12-12 20:07:48.381861 loading file /github/home/.cache/R/BiocFileCache/5c61202c143_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-12-12 20:13:13.093641 loading file /github/home/.cache/R/BiocFileCache/5c77b6ee4a2_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 b72f8c78..f14394bc 100644
--- a/reference/frame_limits.html
+++ b/reference/frame_limits.html
@@ -27,7 +27,7 @@
       
       
         spatialLIBD
-        1.19.1
+        1.19.2
       
     
 
@@ -154,7 +154,7 @@ 
Examples

     ## Obtain the frame limits for one sample
     frame_limits(spe, sampleid = "151673")
 }
-#> 2024-12-12 20:07:50.364298 loading file /github/home/.cache/R/BiocFileCache/1048142167f7_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-12-12 20:13:14.546558 loading file /github/home/.cache/R/BiocFileCache/104970f7ab1e_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 a3b02933..814233e0 100644
--- a/reference/gene_set_enrichment.html
+++ b/reference/gene_set_enrichment.html
@@ -22,7 +22,7 @@
       
       
         spatialLIBD
-        1.19.1
+        1.19.2
       
     
 
@@ -177,7 +177,7 @@ 
Examples

 if (!exists("modeling_results")) {
     modeling_results <- fetch_data(type = "modeling_results")
 }
-#> 2024-12-12 20:08:00.259986 loading file /github/home/.cache/R/BiocFileCache/5c643ff6574_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
+#> 2024-12-12 20:13:23.814359 loading file /github/home/.cache/R/BiocFileCache/5c73806c84a_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 c7cc26fd..9b723965 100644
--- a/reference/gene_set_enrichment_plot.html
+++ b/reference/gene_set_enrichment_plot.html
@@ -18,7 +18,7 @@
       
       
         spatialLIBD
-        1.19.1
+        1.19.2
       
     
 
@@ -178,7 +178,7 @@ 
Examples

 if (!exists("modeling_results")) {
     modeling_results <- fetch_data(type = "modeling_results")
 }
-#> 2024-12-12 20:08:01.751422 loading file /github/home/.cache/R/BiocFileCache/5c643ff6574_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
+#> 2024-12-12 20:13:24.972142 loading file /github/home/.cache/R/BiocFileCache/5c73806c84a_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 257198bd..9941483d 100644
--- a/reference/geom_spatial.html
+++ b/reference/geom_spatial.html
@@ -20,7 +20,7 @@
       
       
         spatialLIBD
-        1.19.1
+        1.19.2
       
     
 
@@ -175,7 +175,7 @@ 
Examples

     ## Clean up
     rm(spe_sub)
 }
-#> 2024-12-12 20:08:03.651475 loading file /github/home/.cache/R/BiocFileCache/1048142167f7_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-12-12 20:13:26.612894 loading file /github/home/.cache/R/BiocFileCache/104970f7ab1e_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
diff --git a/reference/get_colors.html b/reference/get_colors.html index daea5c30..d7960fe1 100644 --- a/reference/get_colors.html +++ b/reference/get_colors.html @@ -18,7 +18,7 @@ spatialLIBD - 1.19.1 + 1.19.2 @@ -105,7 +105,7 @@

Examples


 ## Obtain the necessary data
 if (!exists("sce_layer")) sce_layer <- fetch_data("sce_layer")
-#> 2024-12-12 20:08:14.867719 loading file /github/home/.cache/R/BiocFileCache/5c61202c143_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-12-12 20:13:36.652598 loading file /github/home/.cache/R/BiocFileCache/5c77b6ee4a2_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 b93dd331..ee4e7a98 100644
--- a/reference/img_edit.html
+++ b/reference/img_edit.html
@@ -19,7 +19,7 @@
       
       
         spatialLIBD
-        1.19.1
+        1.19.2
@@ -222,7 +222,7 @@

Examples

x <- img_edit(spe, sampleid = "151507", brightness = 25) plot(x) } -#> 2024-12-12 20:08:16.264234 loading file /github/home/.cache/R/BiocFileCache/1048142167f7_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-12-12 20:13:37.728431 loading file /github/home/.cache/R/BiocFileCache/104970f7ab1e_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 diff --git a/reference/img_update.html b/reference/img_update.html index ccfd0ffa..6dd4b819 100644 --- a/reference/img_update.html +++ b/reference/img_update.html @@ -17,7 +17,7 @@ spatialLIBD - 1.19.1 + 1.19.2 @@ -139,7 +139,7 @@

Examples

## Reduce brightness to 25% and update the imgData() imgData(img_update(spe, sampleid = "151507", brightness = 25)) } -#> 2024-12-12 20:08:27.322526 loading file /github/home/.cache/R/BiocFileCache/1048142167f7_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-12-12 20:13:48.325728 loading file /github/home/.cache/R/BiocFileCache/104970f7ab1e_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 db463905..61742976 100644 --- a/reference/img_update_all.html +++ b/reference/img_update_all.html @@ -19,7 +19,7 @@ spatialLIBD - 1.19.1 + 1.19.2 @@ -138,7 +138,7 @@

Examples

## update the imgData() imgData(img_update_all(spe, brightness = 25)) } -#> 2024-12-12 20:08:37.020438 loading file /github/home/.cache/R/BiocFileCache/1048142167f7_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-12-12 20:13:58.698799 loading file /github/home/.cache/R/BiocFileCache/104970f7ab1e_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/index.html b/reference/index.html index 99adfd9a..d05abc94 100644 --- a/reference/index.html +++ b/reference/index.html @@ -17,7 +17,7 @@ spatialLIBD - 1.19.1 + 1.19.2 diff --git a/reference/layer_boxplot.html b/reference/layer_boxplot.html index 5ba33c11..7b878b7a 100644 --- a/reference/layer_boxplot.html +++ b/reference/layer_boxplot.html @@ -19,7 +19,7 @@ spatialLIBD - 1.19.1 + 1.19.2 @@ -185,9 +185,9 @@

Examples

if (!exists("modeling_results")) { modeling_results <- fetch_data(type = "modeling_results") } -#> 2024-12-12 20:08:49.54346 loading file /github/home/.cache/R/BiocFileCache/5c643ff6574_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1 +#> 2024-12-12 20:14:10.545715 loading file /github/home/.cache/R/BiocFileCache/5c73806c84a_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1 if (!exists("sce_layer")) sce_layer <- fetch_data(type = "sce_layer") -#> 2024-12-12 20:08:50.756527 loading file /github/home/.cache/R/BiocFileCache/5c61202c143_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-12-12 20:14:11.387783 loading file /github/home/.cache/R/BiocFileCache/5c77b6ee4a2_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_matrix_plot.html b/reference/layer_matrix_plot.html index 977af7a9..9ae63397 100644 --- a/reference/layer_matrix_plot.html +++ b/reference/layer_matrix_plot.html @@ -20,7 +20,7 @@ spatialLIBD - 1.19.1 + 1.19.2 diff --git a/reference/layer_stat_cor.html b/reference/layer_stat_cor.html index 2a1e7cdf..82e1456a 100644 --- a/reference/layer_stat_cor.html +++ b/reference/layer_stat_cor.html @@ -17,7 +17,7 @@ spatialLIBD - 1.19.1 + 1.19.2 @@ -161,7 +161,7 @@

Examples

if (!exists("modeling_results")) { modeling_results <- fetch_data(type = "modeling_results") } -#> 2024-12-12 20:08:54.119209 loading file /github/home/.cache/R/BiocFileCache/5c643ff6574_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1 +#> 2024-12-12 20:14:14.297368 loading file /github/home/.cache/R/BiocFileCache/5c73806c84a_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 58ced45d..0556ad9b 100644 --- a/reference/layer_stat_cor_plot.html +++ b/reference/layer_stat_cor_plot.html @@ -22,7 +22,7 @@ spatialLIBD - 1.19.1 + 1.19.2 @@ -169,13 +169,13 @@

Examples

if (!exists("modeling_results")) { modeling_results <- fetch_data(type = "modeling_results") } -#> 2024-12-12 20:08:55.56831 loading file /github/home/.cache/R/BiocFileCache/5c643ff6574_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1 +#> 2024-12-12 20:14:15.418567 loading file /github/home/.cache/R/BiocFileCache/5c73806c84a_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1 ## query spatialDLPFC modeling results query_modeling_results <- fetch_data( type = "spatialDLPFC_Visium_modeling_results" ) -#> 2024-12-12 20:08:56.734446 loading file /github/home/.cache/R/BiocFileCache/104878999b04_modeling_results_BayesSpace_k09.Rdata%3Fdl%3D1 +#> 2024-12-12 20:14:16.2476 loading file /github/home/.cache/R/BiocFileCache/104977134dbb_modeling_results_BayesSpace_k09.Rdata%3Fdl%3D1 ## Compute the correlations cor_stats_layer <- layer_stat_cor( diff --git a/reference/libd_layer_colors.html b/reference/libd_layer_colors.html index eaf1b279..760f52f4 100644 --- a/reference/libd_layer_colors.html +++ b/reference/libd_layer_colors.html @@ -18,7 +18,7 @@ spatialLIBD - 1.19.1 + 1.19.2 diff --git a/reference/locate_images.html b/reference/locate_images.html index 6f1939a8..b1ecc16a 100644 --- a/reference/locate_images.html +++ b/reference/locate_images.html @@ -19,7 +19,7 @@ spatialLIBD - 1.19.1 + 1.19.2 diff --git a/reference/multi_gene_pca.html b/reference/multi_gene_pca.html index 84ebcfd4..405a64bb 100644 --- a/reference/multi_gene_pca.html +++ b/reference/multi_gene_pca.html @@ -22,7 +22,7 @@ spatialLIBD - 1.19.1 + 1.19.2 diff --git a/reference/multi_gene_sparsity.html b/reference/multi_gene_sparsity.html index 53360092..db8dd059 100644 --- a/reference/multi_gene_sparsity.html +++ b/reference/multi_gene_sparsity.html @@ -18,7 +18,7 @@ spatialLIBD - 1.19.1 + 1.19.2 diff --git a/reference/multi_gene_z_score.html b/reference/multi_gene_z_score.html index 9888c85e..8be9ac0e 100644 --- a/reference/multi_gene_z_score.html +++ b/reference/multi_gene_z_score.html @@ -18,7 +18,7 @@ spatialLIBD - 1.19.1 + 1.19.2 diff --git a/reference/prep_stitched_data.html b/reference/prep_stitched_data.html index f5a55a75..5e27e99d 100644 --- a/reference/prep_stitched_data.html +++ b/reference/prep_stitched_data.html @@ -22,7 +22,7 @@ spatialLIBD - 1.19.1 + 1.19.2 diff --git a/reference/read10xVisiumAnalysis.html b/reference/read10xVisiumAnalysis.html index c521eb0c..b96b2175 100644 --- a/reference/read10xVisiumAnalysis.html +++ b/reference/read10xVisiumAnalysis.html @@ -18,7 +18,7 @@ spatialLIBD - 1.19.1 + 1.19.2 diff --git a/reference/read10xVisiumWrapper.html b/reference/read10xVisiumWrapper.html index 426d2d3b..eb68f1db 100644 --- a/reference/read10xVisiumWrapper.html +++ b/reference/read10xVisiumWrapper.html @@ -20,7 +20,7 @@ spatialLIBD - 1.19.1 + 1.19.2 diff --git a/reference/registration_block_cor.html b/reference/registration_block_cor.html index 177d3978..91b94e68 100644 --- a/reference/registration_block_cor.html +++ b/reference/registration_block_cor.html @@ -20,7 +20,7 @@ spatialLIBD - 1.19.1 + 1.19.2 @@ -146,9 +146,9 @@

Examples

#> #> rgstr_> ## Pseudo-bulk #> rgstr_> sce_pseudo <- registration_pseudobulk(sce, "Cell_Cycle", "sample_id", c("age"), min_ncells = NULL) -#> 2024-12-12 20:09:02.846125 make pseudobulk object -#> 2024-12-12 20:09:02.971929 drop lowly expressed genes -#> 2024-12-12 20:09:03.034428 normalize expression +#> 2024-12-12 20:14:22.169827 make pseudobulk object +#> 2024-12-12 20:14:22.290642 drop lowly expressed genes +#> 2024-12-12 20:14:22.349012 normalize expression #> #> rgstr_> colData(sce_pseudo) #> DataFrame with 20 rows and 8 columns @@ -180,7 +180,7 @@

Examples

#> E_S S E 11 #> #> rgstr_> registration_mod <- registration_model(sce_pseudo, "age") -#> 2024-12-12 20:09:03.114902 create model matrix +#> 2024-12-12 20:14:22.426173 create model matrix #> #> rgstr_> head(registration_mod) #> registration_variableG0 registration_variableG1 registration_variableG2M @@ -198,8 +198,8 @@

Examples

#> E_G0 0 20.97006 #> A_G1 0 19.18719 block_cor <- registration_block_cor(sce_pseudo, registration_mod) -#> 2024-12-12 20:09:03.127392 run duplicateCorrelation() -#> 2024-12-12 20:09:04.438658 The estimated correlation is: -0.0187869166526901 +#> 2024-12-12 20:14:22.438107 run duplicateCorrelation() +#> 2024-12-12 20:14:23.737962 The estimated correlation is: -0.0187869166526901 diff --git a/reference/registration_model.html b/reference/registration_model.html index 54d1ed66..d63be0e6 100644 --- a/reference/registration_model.html +++ b/reference/registration_model.html @@ -21,7 +21,7 @@ spatialLIBD - 1.19.1 + 1.19.2 @@ -148,9 +148,9 @@

Examples

#> #> rgstr_> ## Pseudo-bulk #> rgstr_> sce_pseudo <- registration_pseudobulk(sce, "Cell_Cycle", "sample_id", c("age"), min_ncells = NULL) -#> 2024-12-12 20:09:04.749012 make pseudobulk object -#> 2024-12-12 20:09:04.879655 drop lowly expressed genes -#> 2024-12-12 20:09:04.931246 normalize expression +#> 2024-12-12 20:14:24.041494 make pseudobulk object +#> 2024-12-12 20:14:24.170795 drop lowly expressed genes +#> 2024-12-12 20:14:24.215742 normalize expression #> #> rgstr_> colData(sce_pseudo) #> DataFrame with 20 rows and 8 columns @@ -181,7 +181,7 @@

Examples

#> D_S S D 14 #> E_S S E 11 registration_mod <- registration_model(sce_pseudo, "age") -#> 2024-12-12 20:09:05.012922 create model matrix +#> 2024-12-12 20:14:24.289774 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 c113b746..5cdce7c4 100644 --- a/reference/registration_pseudobulk.html +++ b/reference/registration_pseudobulk.html @@ -18,7 +18,7 @@ spatialLIBD - 1.19.1 + 1.19.2 @@ -97,7 +97,9 @@

Arguments

var_registration

A character(1) specifying the colData(sce) variable of interest against which will be used for computing the relevant -statistics.

+statistics. This should be a categorical variable, with all categories +syntaticly valid (could be used as an R variable, no special characters or +leading numbers), ex. 'L1.2', 'celltype2' not 'L1/2' or '2'.

var_sample_id
@@ -159,9 +161,9 @@

Examples

## Pseudo-bulk sce_pseudo <- registration_pseudobulk(sce, "Cell_Cycle", "sample_id", c("age"), min_ncells = NULL) -#> 2024-12-12 20:09:05.350546 make pseudobulk object -#> 2024-12-12 20:09:05.453346 drop lowly expressed genes -#> 2024-12-12 20:09:05.502202 normalize expression +#> 2024-12-12 20:14:24.60953 make pseudobulk object +#> 2024-12-12 20:14:24.705615 drop lowly expressed genes +#> 2024-12-12 20:14:24.751247 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 684b19dd..af99cb4b 100644 --- a/reference/registration_stats_anova.html +++ b/reference/registration_stats_anova.html @@ -20,7 +20,7 @@ spatialLIBD - 1.19.1 + 1.19.2 @@ -180,9 +180,9 @@

Examples

#> #> rgstr_> ## Pseudo-bulk #> rgstr_> sce_pseudo <- registration_pseudobulk(sce, "Cell_Cycle", "sample_id", c("age"), min_ncells = NULL) -#> 2024-12-12 20:09:06.028456 make pseudobulk object -#> 2024-12-12 20:09:06.131246 drop lowly expressed genes -#> 2024-12-12 20:09:06.179501 normalize expression +#> 2024-12-12 20:14:25.256274 make pseudobulk object +#> 2024-12-12 20:14:25.353124 drop lowly expressed genes +#> 2024-12-12 20:14:25.398113 normalize expression #> #> rgstr_> colData(sce_pseudo) #> DataFrame with 20 rows and 8 columns @@ -214,7 +214,7 @@

Examples

#> E_S S E 11 #> #> rgstr_> registration_mod <- registration_model(sce_pseudo, "age") -#> 2024-12-12 20:09:06.257757 create model matrix +#> 2024-12-12 20:14:25.471519 create model matrix #> #> rgstr_> head(registration_mod) #> registration_variableG0 registration_variableG1 registration_variableG2M @@ -233,13 +233,13 @@

Examples

#> A_G1 0 19.18719 #> #> rgst__> block_cor <- registration_block_cor(sce_pseudo, registration_mod) -#> 2024-12-12 20:09:06.269512 run duplicateCorrelation() -#> 2024-12-12 20:09:07.546851 The estimated correlation is: -0.0187869166526901 +#> 2024-12-12 20:14:25.48261 run duplicateCorrelation() +#> 2024-12-12 20:14:26.745378 The estimated correlation is: -0.0187869166526901 results_anova <- registration_stats_anova(sce_pseudo, block_cor, "age", gene_ensembl = "ensembl", gene_name = "gene_name", suffix = "example" ) -#> 2024-12-12 20:09:07.558945 computing F-statistics +#> 2024-12-12 20:14:26.75732 computing F-statistics head(results_anova) #> f_stat_example p_value_example fdr_example AveExpr_example ensembl gene #> 1 0.1328075 0.93918553 0.9951876 5.499488 ENSG1 gene1 @@ -254,7 +254,7 @@

Examples

block_cor = NaN, "age", gene_ensembl = "ensembl", gene_name = "gene_name", suffix = "example" ) -#> 2024-12-12 20:09:07.620734 computing F-statistics +#> 2024-12-12 20:14:26.818832 computing F-statistics head(results_anova_nan) #> f_stat_example p_value_example fdr_example AveExpr_example ensembl gene #> 1 0.1357180 0.93736053 0.9943765 5.499488 ENSG1 gene1 @@ -276,7 +276,7 @@

Examples

covars = NULL, gene_ensembl = "ensembl", gene_name = "gene_name", suffix = "nocovar" ) -#> 2024-12-12 20:09:07.6704 computing F-statistics +#> 2024-12-12 20:14:26.86758 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 26181c26..3bbb7150 100644 --- a/reference/registration_stats_enrichment.html +++ b/reference/registration_stats_enrichment.html @@ -19,7 +19,7 @@ spatialLIBD - 1.19.1 + 1.19.2 @@ -171,9 +171,9 @@

Examples

#> #> rgstr_> ## Pseudo-bulk #> rgstr_> sce_pseudo <- registration_pseudobulk(sce, "Cell_Cycle", "sample_id", c("age"), min_ncells = NULL) -#> 2024-12-12 20:09:08.136167 make pseudobulk object -#> 2024-12-12 20:09:08.237026 drop lowly expressed genes -#> 2024-12-12 20:09:08.285062 normalize expression +#> 2024-12-12 20:14:27.335846 make pseudobulk object +#> 2024-12-12 20:14:27.432925 drop lowly expressed genes +#> 2024-12-12 20:14:27.47867 normalize expression #> #> rgstr_> colData(sce_pseudo) #> DataFrame with 20 rows and 8 columns @@ -205,7 +205,7 @@

Examples

#> E_S S E 11 #> #> rgstr_> registration_mod <- registration_model(sce_pseudo, "age") -#> 2024-12-12 20:09:08.362655 create model matrix +#> 2024-12-12 20:14:27.552789 create model matrix #> #> rgstr_> head(registration_mod) #> registration_variableG0 registration_variableG1 registration_variableG2M @@ -224,14 +224,14 @@

Examples

#> A_G1 0 19.18719 #> #> rgst__> block_cor <- registration_block_cor(sce_pseudo, registration_mod) -#> 2024-12-12 20:09:08.374407 run duplicateCorrelation() -#> 2024-12-12 20:09:09.654462 The estimated correlation is: -0.0187869166526901 +#> 2024-12-12 20:14:27.564003 run duplicateCorrelation() +#> 2024-12-12 20:14:28.838572 The estimated correlation is: -0.0187869166526901 results_enrichment <- registration_stats_enrichment(sce_pseudo, block_cor, "age", gene_ensembl = "ensembl", gene_name = "gene_name" ) -#> 2024-12-12 20:09:09.657928 computing enrichment statistics -#> 2024-12-12 20:09:09.7744 extract and reformat enrichment results +#> 2024-12-12 20:14:28.842156 computing enrichment statistics +#> 2024-12-12 20:14:28.958245 extract and reformat enrichment results head(results_enrichment) #> t_stat_G0 t_stat_G1 t_stat_G2M t_stat_S p_value_G0 p_value_G1 #> Gene_0001 0.1482017 0.5610669 -0.3612235 -0.3458508 0.88374480 0.58130631 @@ -260,8 +260,8 @@

Examples

block_cor = NaN, "age", gene_ensembl = "ensembl", gene_name = "gene_name" ) -#> 2024-12-12 20:09:09.807066 computing enrichment statistics -#> 2024-12-12 20:09:09.937113 extract and reformat enrichment results +#> 2024-12-12 20:14:28.990658 computing enrichment statistics +#> 2024-12-12 20:14:29.122887 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 cd7fbee5..dcf38809 100644 --- a/reference/registration_stats_pairwise.html +++ b/reference/registration_stats_pairwise.html @@ -20,7 +20,7 @@ spatialLIBD - 1.19.1 + 1.19.2 @@ -173,9 +173,9 @@

Examples

#> #> rgstr_> ## Pseudo-bulk #> rgstr_> sce_pseudo <- registration_pseudobulk(sce, "Cell_Cycle", "sample_id", c("age"), min_ncells = NULL) -#> 2024-12-12 20:09:10.287803 make pseudobulk object -#> 2024-12-12 20:09:10.385811 drop lowly expressed genes -#> 2024-12-12 20:09:10.432871 normalize expression +#> 2024-12-12 20:14:29.470541 make pseudobulk object +#> 2024-12-12 20:14:29.566743 drop lowly expressed genes +#> 2024-12-12 20:14:29.61175 normalize expression #> #> rgstr_> colData(sce_pseudo) #> DataFrame with 20 rows and 8 columns @@ -207,7 +207,7 @@

Examples

#> E_S S E 11 #> #> rgstr_> registration_mod <- registration_model(sce_pseudo, "age") -#> 2024-12-12 20:09:10.507925 create model matrix +#> 2024-12-12 20:14:29.684914 create model matrix #> #> rgstr_> head(registration_mod) #> registration_variableG0 registration_variableG1 registration_variableG2M @@ -226,14 +226,14 @@

Examples

#> A_G1 0 19.18719 #> #> rgst__> block_cor <- registration_block_cor(sce_pseudo, registration_mod) -#> 2024-12-12 20:09:10.51942 run duplicateCorrelation() -#> 2024-12-12 20:09:11.789798 The estimated correlation is: -0.0187869166526901 +#> 2024-12-12 20:14:29.696657 run duplicateCorrelation() +#> 2024-12-12 20:14:30.956856 The estimated correlation is: -0.0187869166526901 results_pairwise <- registration_stats_pairwise(sce_pseudo, registration_mod, block_cor, gene_ensembl = "ensembl", gene_name = "gene_name" ) -#> 2024-12-12 20:09:11.791989 running the baseline pairwise model -#> 2024-12-12 20:09:11.809163 computing pairwise statistics +#> 2024-12-12 20:14:30.958621 running the baseline pairwise model +#> 2024-12-12 20:14:30.975643 computing pairwise statistics head(results_pairwise) #> t_stat_G0-G1 t_stat_G0-G2M t_stat_G0-S t_stat_G1-G2M t_stat_G1-S #> Gene_0001 -0.2393683 0.29771391 0.28880637 0.5370822 0.5281747 @@ -277,8 +277,8 @@

Examples

block_cor = NaN, gene_ensembl = "ensembl", gene_name = "gene_name" ) -#> 2024-12-12 20:09:11.875452 running the baseline pairwise model -#> 2024-12-12 20:09:11.893564 computing pairwise statistics +#> 2024-12-12 20:14:31.04176 running the baseline pairwise model +#> 2024-12-12 20:14:31.05934 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 37d41180..4c9bb142 100644 --- a/reference/registration_wrapper.html +++ b/reference/registration_wrapper.html @@ -22,7 +22,7 @@ spatialLIBD - 1.19.1 + 1.19.2 @@ -108,7 +108,9 @@

Arguments

var_registration

A character(1) specifying the colData(sce) variable of interest against which will be used for computing the relevant -statistics.

+statistics. This should be a categorical variable, with all categories +syntaticly valid (could be used as an R variable, no special characters or +leading numbers), ex. 'L1.2', 'celltype2' not 'L1/2' or '2'.

var_sample_id
@@ -205,18 +207,18 @@

Examples

gene_name = "gene_name", suffix = "wrapper" ) -#> 2024-12-12 20:09:12.333615 make pseudobulk object -#> 2024-12-12 20:09:12.430094 dropping 9 pseudo-bulked samples that are below 'min_ncells'. -#> 2024-12-12 20:09:12.443116 drop lowly expressed genes -#> 2024-12-12 20:09:12.489188 normalize expression -#> 2024-12-12 20:09:12.546815 create model matrix -#> 2024-12-12 20:09:12.557324 run duplicateCorrelation() -#> 2024-12-12 20:09:14.988015 The estimated correlation is: -0.0783081238514531 -#> 2024-12-12 20:09:14.990538 computing enrichment statistics -#> 2024-12-12 20:09:15.106225 extract and reformat enrichment results -#> 2024-12-12 20:09:15.131998 running the baseline pairwise model -#> 2024-12-12 20:09:15.15045 computing pairwise statistics -#> 2024-12-12 20:09:15.224735 computing F-statistics +#> 2024-12-12 20:14:31.495134 make pseudobulk object +#> 2024-12-12 20:14:31.588071 dropping 9 pseudo-bulked samples that are below 'min_ncells'. +#> 2024-12-12 20:14:31.600617 drop lowly expressed genes +#> 2024-12-12 20:14:31.646827 normalize expression +#> 2024-12-12 20:14:31.705572 create model matrix +#> 2024-12-12 20:14:31.715721 run duplicateCorrelation() +#> 2024-12-12 20:14:34.131909 The estimated correlation is: -0.0783081238514531 +#> 2024-12-12 20:14:34.134398 computing enrichment statistics +#> 2024-12-12 20:14:34.246299 extract and reformat enrichment results +#> 2024-12-12 20:14:34.271317 running the baseline pairwise model +#> 2024-12-12 20:14:34.289143 computing pairwise statistics +#> 2024-12-12 20:14:34.361598 computing F-statistics ## Explore the results from registration_wrapper() class(example_modeling_results) diff --git a/reference/run_app.html b/reference/run_app.html index 314c500c..0ce84dde 100644 --- a/reference/run_app.html +++ b/reference/run_app.html @@ -19,7 +19,7 @@ spatialLIBD - 1.19.1 + 1.19.2 diff --git a/reference/sce_to_spe.html b/reference/sce_to_spe.html index 464b5355..f2c7a4a9 100644 --- a/reference/sce_to_spe.html +++ b/reference/sce_to_spe.html @@ -21,7 +21,7 @@ spatialLIBD - 1.19.1 + 1.19.2 @@ -127,7 +127,7 @@

Examples

## Transform it to a SpatialExperiment object spe <- sce_to_spe(sce) } -#> 2024-12-12 20:09:17.436095 loading file /github/home/.cache/R/BiocFileCache/1048142167f7_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-12-12 20:14:36.016868 loading file /github/home/.cache/R/BiocFileCache/104970f7ab1e_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 8ee0d0e1..03e7a5e6 100644 --- a/reference/sig_genes_extract.html +++ b/reference/sig_genes_extract.html @@ -21,7 +21,7 @@ spatialLIBD - 1.19.1 + 1.19.2 @@ -157,9 +157,9 @@

Examples

if (!exists("modeling_results")) { modeling_results <- fetch_data(type = "modeling_results") } -#> 2024-12-12 20:09:26.474269 loading file /github/home/.cache/R/BiocFileCache/5c643ff6574_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1 +#> 2024-12-12 20:14:44.227529 loading file /github/home/.cache/R/BiocFileCache/5c73806c84a_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1 if (!exists("sce_layer")) sce_layer <- fetch_data(type = "sce_layer") -#> 2024-12-12 20:09:27.633036 loading file /github/home/.cache/R/BiocFileCache/5c61202c143_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-12-12 20:14:45.070311 loading file /github/home/.cache/R/BiocFileCache/5c77b6ee4a2_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 fe1a4afa..13e28f95 100644 --- a/reference/sig_genes_extract_all.html +++ b/reference/sig_genes_extract_all.html @@ -19,7 +19,7 @@ spatialLIBD - 1.19.1 + 1.19.2 @@ -129,9 +129,9 @@

Examples

if (!exists("modeling_results")) { modeling_results <- fetch_data(type = "modeling_results") } -#> 2024-12-12 20:09:30.942388 loading file /github/home/.cache/R/BiocFileCache/5c643ff6574_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1 +#> 2024-12-12 20:14:48.113463 loading file /github/home/.cache/R/BiocFileCache/5c73806c84a_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1 if (!exists("sce_layer")) sce_layer <- fetch_data(type = "sce_layer") -#> 2024-12-12 20:09:32.070068 loading file /github/home/.cache/R/BiocFileCache/5c61202c143_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-12-12 20:14:48.916816 loading file /github/home/.cache/R/BiocFileCache/5c77b6ee4a2_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/sort_clusters.html b/reference/sort_clusters.html index 228cd0cc..9b755504 100644 --- a/reference/sort_clusters.html +++ b/reference/sort_clusters.html @@ -19,7 +19,7 @@ spatialLIBD - 1.19.1 + 1.19.2 diff --git a/reference/spatialLIBD-package.html b/reference/spatialLIBD-package.html index 5e25d3ed..07550d21 100644 --- a/reference/spatialLIBD-package.html +++ b/reference/spatialLIBD-package.html @@ -18,7 +18,7 @@ spatialLIBD - 1.19.1 + 1.19.2 diff --git a/reference/tstats_Human_DLPFC_snRNAseq_Nguyen_topLayer.html b/reference/tstats_Human_DLPFC_snRNAseq_Nguyen_topLayer.html index b52fc544..84267304 100644 --- a/reference/tstats_Human_DLPFC_snRNAseq_Nguyen_topLayer.html +++ b/reference/tstats_Human_DLPFC_snRNAseq_Nguyen_topLayer.html @@ -23,7 +23,7 @@ spatialLIBD - 1.19.1 + 1.19.2 diff --git a/reference/vis_clus.html b/reference/vis_clus.html index 79cde708..4c2a2ab5 100644 --- a/reference/vis_clus.html +++ b/reference/vis_clus.html @@ -19,7 +19,7 @@ spatialLIBD - 1.19.1 + 1.19.2 @@ -242,7 +242,7 @@

Examples

) print(p4) } -#> 2024-12-12 20:09:34.822872 loading file /github/home/.cache/R/BiocFileCache/1048142167f7_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-12-12 20:14:51.148904 loading file /github/home/.cache/R/BiocFileCache/104970f7ab1e_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 2423f461..b0b3315a 100644 --- a/reference/vis_clus_p.html +++ b/reference/vis_clus_p.html @@ -20,7 +20,7 @@ spatialLIBD - 1.19.1 + 1.19.2 @@ -202,7 +202,7 @@

Examples

## Clean up rm(spe_sub) } -#> 2024-12-12 20:09:48.121684 loading file /github/home/.cache/R/BiocFileCache/1048142167f7_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-12-12 20:15:04.267328 loading file /github/home/.cache/R/BiocFileCache/104970f7ab1e_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 diff --git a/reference/vis_gene.html b/reference/vis_gene.html index 5abb9064..208e79b6 100644 --- a/reference/vis_gene.html +++ b/reference/vis_gene.html @@ -20,7 +20,7 @@ spatialLIBD - 1.19.1 + 1.19.2 @@ -341,7 +341,7 @@

Examples

) print(p8) } -#> 2024-12-12 20:09:58.30165 loading file /github/home/.cache/R/BiocFileCache/1048142167f7_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-12-12 20:15:14.094575 loading file /github/home/.cache/R/BiocFileCache/104970f7ab1e_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 ef3295d3..f6e58bc1 100644 --- a/reference/vis_gene_p.html +++ b/reference/vis_gene_p.html @@ -21,7 +21,7 @@ spatialLIBD - 1.19.1 + 1.19.2 @@ -215,7 +215,7 @@

Examples

## Clean up rm(spe_sub) } -#> 2024-12-12 20:10:16.076427 loading file /github/home/.cache/R/BiocFileCache/1048142167f7_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-12-12 20:15:31.510904 loading file /github/home/.cache/R/BiocFileCache/104970f7ab1e_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 ab65ed9f..6697fdfa 100644 --- a/reference/vis_grid_clus.html +++ b/reference/vis_grid_clus.html @@ -19,7 +19,7 @@ spatialLIBD - 1.19.1 + 1.19.2 @@ -237,7 +237,7 @@

Examples

## for subject 3 cowplot::plot_grid(plotlist = p_list, ncol = 2) } -#> 2024-12-12 20:10:26.460706 loading file /github/home/.cache/R/BiocFileCache/1048142167f7_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-12-12 20:15:41.200938 loading file /github/home/.cache/R/BiocFileCache/104970f7ab1e_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 0ddcbc76..d3a67471 100644 --- a/reference/vis_grid_gene.html +++ b/reference/vis_grid_gene.html @@ -20,7 +20,7 @@ spatialLIBD - 1.19.1 + 1.19.2 @@ -256,7 +256,7 @@

Examples

## for subject 3 cowplot::plot_grid(plotlist = p_list, ncol = 2) } -#> 2024-12-12 20:10:37.901532 loading file /github/home/.cache/R/BiocFileCache/1048142167f7_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-12-12 20:15:52.020228 loading file /github/home/.cache/R/BiocFileCache/104970f7ab1e_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1