From 225caeaec20301a0fb49b60a501414fafb39f0fd Mon Sep 17 00:00:00 2001 From: lcolladotor Date: Thu, 12 Dec 2024 20:35:36 +0000 Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20LieberIn?= =?UTF-8?q?stitute/spatialLIBD@4607fa7cc0523886360384e25204a0a352cc810d=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 | 9 +++-- 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 | 8 ++--- reference/registration_stats_anova.html | 20 +++++------ reference/registration_stats_enrichment.html | 22 ++++++------ reference/registration_stats_pairwise.html | 22 ++++++------ reference/registration_wrapper.html | 26 +++++++------- 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, 214 insertions(+), 209 deletions(-) diff --git a/404.html b/404.html index 9e63ee19..a3f0a920 100644 --- a/404.html +++ b/404.html @@ -40,7 +40,7 @@ spatialLIBD - 1.19.2 + 1.19.3 diff --git a/CODE_OF_CONDUCT.html b/CODE_OF_CONDUCT.html index 6fe03f99..3d5a65b1 100644 --- a/CODE_OF_CONDUCT.html +++ b/CODE_OF_CONDUCT.html @@ -17,7 +17,7 @@ spatialLIBD - 1.19.2 + 1.19.3 diff --git a/CONTRIBUTING.html b/CONTRIBUTING.html index 259f4a54..48e07319 100644 --- a/CONTRIBUTING.html +++ b/CONTRIBUTING.html @@ -17,7 +17,7 @@ spatialLIBD - 1.19.2 + 1.19.3 diff --git a/SUPPORT.html b/SUPPORT.html index 2f46428c..d5dd1ba4 100644 --- a/SUPPORT.html +++ b/SUPPORT.html @@ -17,7 +17,7 @@ spatialLIBD - 1.19.2 + 1.19.3 diff --git a/articles/TenX_data_download.html b/articles/TenX_data_download.html index eff7872f..32b60ac0 100644 --- a/articles/TenX_data_download.html +++ b/articles/TenX_data_download.html @@ -39,7 +39,7 @@ spatialLIBD - 1.19.2 + 1.19.3 @@ -532,7 +532,7 @@

From Gencode## Show the GTF cache location gtf_cache #> BFC4 -#> "/github/home/.cache/R/BiocFileCache/5c6253e2f85_gencode.v32.annotation.gtf.gz" +#> "/github/home/.cache/R/BiocFileCache/5c814c875c8_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 20:33:13.426251 SpatialExperiment::read10xVisium: reading basic data from SpaceRanger -#> 2024-12-12 20:33:23.429828 read10xVisiumAnalysis: reading analysis output from SpaceRanger -#> 2024-12-12 20:33:24.445329 add10xVisiumAnalysis: adding analysis output from SpaceRanger -#> 2024-12-12 20:33:24.589185 rtracklayer::import: reading the reference GTF file -#> 2024-12-12 20:33:48.909886 adding gene information to the SPE object +#> 2024-12-12 20:34:45.702653 SpatialExperiment::read10xVisium: reading basic data from SpaceRanger +#> 2024-12-12 20:34:55.56971 read10xVisiumAnalysis: reading analysis output from SpaceRanger +#> 2024-12-12 20:34:56.611381 add10xVisiumAnalysis: adding analysis output from SpaceRanger +#> 2024-12-12 20:34:56.756241 rtracklayer::import: reading the reference GTF file +#> 2024-12-12 20:35:21.276621 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 20:33:50.291696 adding information used by spatialLIBD +#> 2024-12-12 20:35:22.717394 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 20:33:51 UTC"
+
#> [1] "2024-12-12 20:35:23 UTC"

Wallclock time spent generating the vignette.

-
#> Time difference of 1.625 mins
+
#> Time difference of 1.628 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          * 1.19.2    2024-12-12 [1] Bioconductor
+#>  spatialLIBD          * 1.19.3    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 1651e732..739be3da 100644
--- a/articles/guide_to_spatial_registration.html
+++ b/articles/guide_to_spatial_registration.html
@@ -39,7 +39,7 @@
       
       
         spatialLIBD
-        1.19.2
+        1.19.3
       
     
 
@@ -288,7 +288,7 @@ 
Spatial Reference
 ## get reference layer enrichment statistics
 layer_modeling_results <- fetch_data(type = "modeling_results")
-#> 2024-12-12 20:30:19.027271 loading file /github/home/.cache/R/BiocFileCache/5c63873b16e_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
+#> 2024-12-12 20:31:51.967881 loading file /github/home/.cache/R/BiocFileCache/5c8368bad58_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 20:30:26.828226 make pseudobulk object
-#> 2024-12-12 20:30:28.474782 dropping 13 pseudo-bulked samples that are below 'min_ncells'.
-#> 2024-12-12 20:30:28.5199 drop lowly expressed genes
-#> 2024-12-12 20:30:28.671495 normalize expression
-#> 2024-12-12 20:30:30.128725 create model matrix
-#> 2024-12-12 20:30:30.152171 run duplicateCorrelation()
-#> 2024-12-12 20:30:43.097588 The estimated correlation is: 0.138734774807097
-#> 2024-12-12 20:30:43.10026 computing enrichment statistics
-#> 2024-12-12 20:30:44.295868 extract and reformat enrichment results
-#> 2024-12-12 20:30:44.351039 running the baseline pairwise model
-#> 2024-12-12 20:30:44.496462 computing pairwise statistics
-#> 2024-12-12 20:30:46.591945 computing F-statistics

+#> 2024-12-12 20:32:00.035087 make pseudobulk object
+#> 2024-12-12 20:32:01.709264 dropping 13 pseudo-bulked samples that are below 'min_ncells'.
+#> 2024-12-12 20:32:01.755982 drop lowly expressed genes
+#> 2024-12-12 20:32:01.926612 normalize expression
+#> 2024-12-12 20:32:03.518439 create model matrix
+#> 2024-12-12 20:32:03.542289 run duplicateCorrelation()
+#> 2024-12-12 20:32:16.649376 The estimated correlation is: 0.138734774807097
+#> 2024-12-12 20:32:16.652071 computing enrichment statistics
+#> 2024-12-12 20:32:17.900587 extract and reformat enrichment results
+#> 2024-12-12 20:32:17.957854 running the baseline pairwise model
+#> 2024-12-12 20:32:18.103082 computing pairwise statistics
+#> 2024-12-12 20:32:20.252614 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 20:30:49 UTC"
+
#> [1] "2024-12-12 20:32:23 UTC"

Wallclock time spent generating the vignette.

-
#> Time difference of 43.108 secs
+
#> Time difference of 43.59 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          * 1.19.2    2024-12-12 [1] Bioconductor
+#>  spatialLIBD          * 1.19.3    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 135201eb..5d57afa4 100644
--- a/articles/index.html
+++ b/articles/index.html
@@ -17,7 +17,7 @@
       
       
         spatialLIBD
-        1.19.2
+        1.19.3
       
     
 
diff --git a/articles/multi_gene_plots.html b/articles/multi_gene_plots.html
index 7022ad6c..8764e910 100644
--- a/articles/multi_gene_plots.html
+++ b/articles/multi_gene_plots.html
@@ -39,7 +39,7 @@
       
       
         spatialLIBD
-        1.19.2
+        1.19.3
       
     
 
@@ -195,9 +195,9 @@ 
Plotting One Gene
 modeling_results <- fetch_data(type = "modeling_results")
-#> 2024-12-12 20:31:13.480651 loading file /github/home/.cache/R/BiocFileCache/5c63873b16e_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
+#> 2024-12-12 20:32:47.318725 loading file /github/home/.cache/R/BiocFileCache/5c8368bad58_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
 sce_layer <- fetch_data(type = "sce_layer")
-#> 2024-12-12 20:31:14.735238 loading file /github/home/.cache/R/BiocFileCache/5c631378225_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-12-12 20:32:48.156547 loading file /github/home/.cache/R/BiocFileCache/5c84ecba40c_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 20:31:30 UTC"

+
#> [1] "2024-12-12 20:33:03 UTC"

 
Wallclock time spent generating the vignette.

-
#> Time difference of 36.553 secs

+
#> Time difference of 35.604 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          * 1.19.2    2024-12-12 [1] Bioconductor
+#>  spatialLIBD          * 1.19.3    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 876c91f5..07ca339a 100644
--- a/articles/spatialLIBD.html
+++ b/articles/spatialLIBD.html
@@ -39,7 +39,7 @@
       
       
         spatialLIBD
-        1.19.2
+        1.19.3
       
     
 
@@ -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 20:31:46.360316 loading file /github/home/.cache/R/BiocFileCache/5c6365b51bb_sce_sub_for_vignette.Rdata%3Fdl%3D1
+#> 2024-12-12 20:33:19.306959 loading file /github/home/.cache/R/BiocFileCache/5c82f8b5ea6_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 20:31:51.288139 loading file /github/home/.cache/R/BiocFileCache/5c631378225_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-12-12 20:33:23.348428 loading file /github/home/.cache/R/BiocFileCache/5c84ecba40c_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
 modeling_results <- fetch_data("modeling_results", eh = ehub)
-#> 2024-12-12 20:31:51.716489 loading file /github/home/.cache/R/BiocFileCache/5c63873b16e_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1

+#> 2024-12-12 20:33:23.78055 loading file /github/home/.cache/R/BiocFileCache/5c8368bad58_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 
-#>   9.190   0.381   9.584
+#>   9.449   0.336   9.798
 
 ## 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 20:32:09 UTC"

+
#> [1] "2024-12-12 20:33:41 UTC"

 
Wallclock time spent generating the vignette.

-
#> Time difference of 35.616 secs

+
#> Time difference of 34.535 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          * 1.19.2    2024-12-12 [1] Bioconductor
+#>  spatialLIBD          * 1.19.3    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 a82f81ea..9a180d09 100644
--- a/authors.html
+++ b/authors.html
@@ -17,7 +17,7 @@
       
       
         spatialLIBD
-        1.19.2
+        1.19.3
       
     
 
diff --git a/index.html b/index.html
index 35f54314..71ffb15d 100644
--- a/index.html
+++ b/index.html
@@ -41,7 +41,7 @@
       
       
         spatialLIBD
-        1.19.2
+        1.19.3
       
     
 
diff --git a/news/index.html b/news/index.html
index 0c83d694..516885bf 100644
--- a/news/index.html
+++ b/news/index.html
@@ -17,7 +17,7 @@
       
       
         spatialLIBD
-        1.19.2
+        1.19.3
       
     
 
@@ -66,10 +66,15 @@ 
Changelog 

       Source: NEWS.md
     
 
+    

+
spatialLIBD 1.19.3

+
BUG FIXES

+

     

 
spatialLIBD 1.19.2

 
BUG FIXES

-

     

 
spatialLIBD 1.19.1

diff --git a/pkgdown.yml b/pkgdown.yml
index aed2fdde..f2de69b8 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: 2024-12-12T20:25Z
+last_built: 2024-12-12T20:27Z
diff --git a/reference/add10xVisiumAnalysis.html b/reference/add10xVisiumAnalysis.html
index 6872b180..2cd6bd06 100644
--- a/reference/add10xVisiumAnalysis.html
+++ b/reference/add10xVisiumAnalysis.html
@@ -19,7 +19,7 @@
       
       
         spatialLIBD
-        1.19.2
+        1.19.3
       
     

 
diff --git a/reference/add_images.html b/reference/add_images.html
index 88c5171c..660fa0a6 100644
--- a/reference/add_images.html
+++ b/reference/add_images.html
@@ -25,7 +25,7 @@
       
       
         spatialLIBD
-        1.19.2
+        1.19.3
       
     
 
@@ -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 20:25:51.037023 loading file /github/home/.cache/R/BiocFileCache/104729279b36_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
-#> 2024-12-12 20:26:02.086305 adding image for sample 151507
-#> 2024-12-12 20:26:03.448337 adding image for sample 151508
+#> 2024-12-12 20:27:39.034866 loading file /github/home/.cache/R/BiocFileCache/1049eae8491_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-12-12 20:27:50.068299 adding image for sample 151507
+#> 2024-12-12 20:27:50.70745 adding image for sample 151508
 #> Warning: No image was found for sample: 151508
-#> 2024-12-12 20:26:03.449069 adding image for sample 151509
+#> 2024-12-12 20:27:50.70827 adding image for sample 151509
 #> Warning: No image was found for sample: 151509
-#> 2024-12-12 20:26:03.449585 adding image for sample 151510
+#> 2024-12-12 20:27:50.708853 adding image for sample 151510
 #> Warning: No image was found for sample: 151510
-#> 2024-12-12 20:26:03.450067 adding image for sample 151669
+#> 2024-12-12 20:27:50.709384 adding image for sample 151669
 #> Warning: No image was found for sample: 151669
-#> 2024-12-12 20:26:03.450534 adding image for sample 151670
+#> 2024-12-12 20:27:50.709886 adding image for sample 151670
 #> Warning: No image was found for sample: 151670
-#> 2024-12-12 20:26:03.450995 adding image for sample 151671
+#> 2024-12-12 20:27:50.710389 adding image for sample 151671
 #> Warning: No image was found for sample: 151671
-#> 2024-12-12 20:26:03.451465 adding image for sample 151672
+#> 2024-12-12 20:27:50.710871 adding image for sample 151672
 #> Warning: No image was found for sample: 151672
-#> 2024-12-12 20:26:03.451933 adding image for sample 151673
+#> 2024-12-12 20:27:50.711337 adding image for sample 151673
 #> Warning: No image was found for sample: 151673
-#> 2024-12-12 20:26:03.452389 adding image for sample 151674
+#> 2024-12-12 20:27:50.711798 adding image for sample 151674
 #> Warning: No image was found for sample: 151674
-#> 2024-12-12 20:26:03.452857 adding image for sample 151675
+#> 2024-12-12 20:27:50.712255 adding image for sample 151675
 #> Warning: No image was found for sample: 151675
-#> 2024-12-12 20:26:03.453321 adding image for sample 151676
+#> 2024-12-12 20:27:50.712736 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 2d4fdb89..fa3cb8ae 100644
--- a/reference/add_key.html
+++ b/reference/add_key.html
@@ -19,7 +19,7 @@
       
       
         spatialLIBD
-        1.19.2
+        1.19.3
       
     
 
@@ -124,7 +124,7 @@ 
Examples

     spe$key_original <- NULL
     head(spe$key)
 }
-#> 2024-12-12 20:26:06.121516 loading file /github/home/.cache/R/BiocFileCache/104729279b36_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-12-12 20:27:53.066181 loading file /github/home/.cache/R/BiocFileCache/1049eae8491_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 8442e388..e5c6b123 100644
--- a/reference/add_qc_metrics.html
+++ b/reference/add_qc_metrics.html
@@ -21,7 +21,7 @@
       
       
         spatialLIBD
-        1.19.2
+        1.19.3
       
     
 
@@ -144,7 +144,7 @@ 
Author

     
Examples

     
## Obtain the necessary data
 spe_pre_qc <- fetch_data("spatialDLPFC_Visium_example_subset")
-#> 2024-12-12 20:26:17.92422 loading file /github/home/.cache/R/BiocFileCache/5c66cdcea20_spatialDLPFC_spe_subset_example.rds%3Fdl%3D1
+#> 2024-12-12 20:28:04.064539 loading file /github/home/.cache/R/BiocFileCache/5c84e2fd1a9_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 63cdc78a..2a6e3de5 100644
--- a/reference/annotate_registered_clusters.html
+++ b/reference/annotate_registered_clusters.html
@@ -21,7 +21,7 @@
       
       
         spatialLIBD
-        1.19.2
+        1.19.3
       
     

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

 if (!exists("modeling_results")) {
     modeling_results <- fetch_data(type = "modeling_results")
 }
-#> 2024-12-12 20:26:29.817602 loading file /github/home/.cache/R/BiocFileCache/5c63873b16e_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
+#> 2024-12-12 20:28:15.758414 loading file /github/home/.cache/R/BiocFileCache/5c8368bad58_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 a3d75e20..fc7bca81 100644
--- a/reference/check_modeling_results.html
+++ b/reference/check_modeling_results.html
@@ -18,7 +18,7 @@
       
       
         spatialLIBD
-        1.19.2
+        1.19.3
       
     
 
@@ -109,7 +109,7 @@ 
Examples

 if (!exists("modeling_results")) {
     modeling_results <- fetch_data(type = "modeling_results")
 }
-#> 2024-12-12 20:26:31.137701 loading file /github/home/.cache/R/BiocFileCache/5c63873b16e_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
+#> 2024-12-12 20:28:16.713844 loading file /github/home/.cache/R/BiocFileCache/5c8368bad58_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 a00e7898..03fc5ddc 100644
--- a/reference/check_sce.html
+++ b/reference/check_sce.html
@@ -20,7 +20,7 @@
       
       
         spatialLIBD
-        1.19.2
+        1.19.3
       
     
 
@@ -131,7 +131,7 @@ 
Examples

     ## Check the object
     check_sce(sce_example)
 }
-#> 2024-12-12 20:26:32.390597 loading file /github/home/.cache/R/BiocFileCache/5c6365b51bb_sce_sub_for_vignette.Rdata%3Fdl%3D1
+#> 2024-12-12 20:28:17.633653 loading file /github/home/.cache/R/BiocFileCache/5c82f8b5ea6_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 2f4dd344..c8c01bac 100644
--- a/reference/check_sce_layer.html
+++ b/reference/check_sce_layer.html
@@ -18,7 +18,7 @@
       
       
         spatialLIBD
-        1.19.2
+        1.19.3
       
     
 
@@ -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 20:26:34.924479 loading file /github/home/.cache/R/BiocFileCache/5c631378225_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-12-12 20:28:19.834515 loading file /github/home/.cache/R/BiocFileCache/5c84ecba40c_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 dcba7638..0bd25127 100644
--- a/reference/check_spe.html
+++ b/reference/check_spe.html
@@ -18,7 +18,7 @@
       
       
         spatialLIBD
-        1.19.2
+        1.19.3
       
     
 
@@ -123,7 +123,7 @@ 
Examples

     ## Check the object
     check_spe(spe)
 }
-#> 2024-12-12 20:26:36.310702 loading file /github/home/.cache/R/BiocFileCache/104729279b36_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-12-12 20:28:20.905576 loading file /github/home/.cache/R/BiocFileCache/1049eae8491_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 d44a5d63..c1687d38 100644
--- a/reference/cluster_export.html
+++ b/reference/cluster_export.html
@@ -21,7 +21,7 @@
       
       
         spatialLIBD
-        1.19.2
+        1.19.3
       
     
 
@@ -134,7 +134,7 @@ 
Examples

     cluster_export(spe, "spatialLIBD")
     cluster_export(spe, "GraphBased")
 }
-#> 2024-12-12 20:26:46.127632 loading file /github/home/.cache/R/BiocFileCache/104729279b36_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-12-12 20:28:30.283198 loading file /github/home/.cache/R/BiocFileCache/1049eae8491_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 68a52fa1..5e9e5ba5 100644
--- a/reference/cluster_import.html
+++ b/reference/cluster_import.html
@@ -20,7 +20,7 @@
       
       
         spatialLIBD
-        1.19.2
+        1.19.3
       
     
 
@@ -137,11 +137,11 @@ 
Examples

     ## Re-import them
     colData(cluster_import(spe))
 }
-#> 2024-12-12 20:26:56.632989 loading file /github/home/.cache/R/BiocFileCache/104729279b36_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-12-12 20:28:40.741707 loading file /github/home/.cache/R/BiocFileCache/1049eae8491_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
 #> Overwriting 'spe$key'. Set 'overwrite = FALSE' if you do not want to overwrite it.
-#> Warning: '/tmp/Rtmp1JiPIl/exported_clusters/spatialLIBD' already exists
+#> Warning: '/tmp/RtmpkdK6id/exported_clusters/spatialLIBD' already exists
 #> Overwriting 'spe$key'. Set 'overwrite = FALSE' if you do not want to overwrite it.
-#> Warning: '/tmp/Rtmp1JiPIl/exported_clusters/GraphBased' already exists
+#> Warning: '/tmp/RtmpkdK6id/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 fd08c505..3ebf7a8f 100644
--- a/reference/enough_ram.html
+++ b/reference/enough_ram.html
@@ -17,7 +17,7 @@
       
       
         spatialLIBD
-        1.19.2
+        1.19.3
       
     
 
diff --git a/reference/fetch_data.html b/reference/fetch_data.html
index cc684f42..e1b0b3d2 100644
--- a/reference/fetch_data.html
+++ b/reference/fetch_data.html
@@ -25,7 +25,7 @@
       
       
         spatialLIBD
-        1.19.2
+        1.19.3
       
     
 
@@ -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 20:27:08.14248 loading file /github/home/.cache/R/BiocFileCache/5c631378225_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-12-12 20:28:51.901223 loading file /github/home/.cache/R/BiocFileCache/5c84ecba40c_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 884bf9d7..a3ce1180 100644
--- a/reference/frame_limits.html
+++ b/reference/frame_limits.html
@@ -27,7 +27,7 @@
       
       
         spatialLIBD
-        1.19.2
+        1.19.3
       
     
 
@@ -154,7 +154,7 @@ 
Examples

     ## Obtain the frame limits for one sample
     frame_limits(spe, sampleid = "151673")
 }
-#> 2024-12-12 20:27:10.138788 loading file /github/home/.cache/R/BiocFileCache/104729279b36_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-12-12 20:28:53.428138 loading file /github/home/.cache/R/BiocFileCache/1049eae8491_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 d81ed728..dc41cf6c 100644
--- a/reference/gene_set_enrichment.html
+++ b/reference/gene_set_enrichment.html
@@ -22,7 +22,7 @@
       
       
         spatialLIBD
-        1.19.2
+        1.19.3
       
     
 
@@ -177,7 +177,7 @@ 
Examples

 if (!exists("modeling_results")) {
     modeling_results <- fetch_data(type = "modeling_results")
 }
-#> 2024-12-12 20:27:20.126591 loading file /github/home/.cache/R/BiocFileCache/5c63873b16e_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
+#> 2024-12-12 20:29:02.664232 loading file /github/home/.cache/R/BiocFileCache/5c8368bad58_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 8f047b3d..29af015e 100644
--- a/reference/gene_set_enrichment_plot.html
+++ b/reference/gene_set_enrichment_plot.html
@@ -18,7 +18,7 @@
       
       
         spatialLIBD
-        1.19.2
+        1.19.3
       
     
 
@@ -178,7 +178,7 @@ 
Examples

 if (!exists("modeling_results")) {
     modeling_results <- fetch_data(type = "modeling_results")
 }
-#> 2024-12-12 20:27:21.613384 loading file /github/home/.cache/R/BiocFileCache/5c63873b16e_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
+#> 2024-12-12 20:29:03.78116 loading file /github/home/.cache/R/BiocFileCache/5c8368bad58_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 df164f8f..8eec7af9 100644
--- a/reference/geom_spatial.html
+++ b/reference/geom_spatial.html
@@ -20,7 +20,7 @@
       
       
         spatialLIBD
-        1.19.2
+        1.19.3
       
     
 
@@ -175,7 +175,7 @@ 
Examples

     ## Clean up
     rm(spe_sub)
 }
-#> 2024-12-12 20:27:23.522083 loading file /github/home/.cache/R/BiocFileCache/104729279b36_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-12-12 20:29:05.316495 loading file /github/home/.cache/R/BiocFileCache/1049eae8491_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
diff --git a/reference/get_colors.html b/reference/get_colors.html index e39d7f24..1ce0cd33 100644 --- a/reference/get_colors.html +++ b/reference/get_colors.html @@ -18,7 +18,7 @@ spatialLIBD - 1.19.2 + 1.19.3 @@ -105,7 +105,7 @@

Examples


 ## Obtain the necessary data
 if (!exists("sce_layer")) sce_layer <- fetch_data("sce_layer")
-#> 2024-12-12 20:27:34.274961 loading file /github/home/.cache/R/BiocFileCache/5c631378225_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-12-12 20:29:15.285175 loading file /github/home/.cache/R/BiocFileCache/5c84ecba40c_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 19b88678..47f2391d 100644
--- a/reference/img_edit.html
+++ b/reference/img_edit.html
@@ -19,7 +19,7 @@
       
       
         spatialLIBD
-        1.19.2
+        1.19.3
@@ -222,7 +222,7 @@

Examples

x <- img_edit(spe, sampleid = "151507", brightness = 25) plot(x) } -#> 2024-12-12 20:27:35.745717 loading file /github/home/.cache/R/BiocFileCache/104729279b36_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-12-12 20:29:16.31568 loading file /github/home/.cache/R/BiocFileCache/1049eae8491_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 diff --git a/reference/img_update.html b/reference/img_update.html index acb40956..4edbda75 100644 --- a/reference/img_update.html +++ b/reference/img_update.html @@ -17,7 +17,7 @@ spatialLIBD - 1.19.2 + 1.19.3 @@ -139,7 +139,7 @@

Examples

## Reduce brightness to 25% and update the imgData() imgData(img_update(spe, sampleid = "151507", brightness = 25)) } -#> 2024-12-12 20:27:46.897288 loading file /github/home/.cache/R/BiocFileCache/104729279b36_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-12-12 20:29:27.710752 loading file /github/home/.cache/R/BiocFileCache/1049eae8491_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 1979f61d..7f87efcd 100644 --- a/reference/img_update_all.html +++ b/reference/img_update_all.html @@ -19,7 +19,7 @@ spatialLIBD - 1.19.2 + 1.19.3 @@ -138,7 +138,7 @@

Examples

## update the imgData() imgData(img_update_all(spe, brightness = 25)) } -#> 2024-12-12 20:27:56.627822 loading file /github/home/.cache/R/BiocFileCache/104729279b36_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-12-12 20:29:36.965805 loading file /github/home/.cache/R/BiocFileCache/1049eae8491_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 d05abc94..e7976b67 100644 --- a/reference/index.html +++ b/reference/index.html @@ -17,7 +17,7 @@ spatialLIBD - 1.19.2 + 1.19.3 diff --git a/reference/layer_boxplot.html b/reference/layer_boxplot.html index 51dfc4f9..de7bd041 100644 --- a/reference/layer_boxplot.html +++ b/reference/layer_boxplot.html @@ -19,7 +19,7 @@ spatialLIBD - 1.19.2 + 1.19.3 @@ -185,9 +185,9 @@

Examples

if (!exists("modeling_results")) { modeling_results <- fetch_data(type = "modeling_results") } -#> 2024-12-12 20:28:08.813854 loading file /github/home/.cache/R/BiocFileCache/5c63873b16e_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1 +#> 2024-12-12 20:29:48.777129 loading file /github/home/.cache/R/BiocFileCache/5c8368bad58_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1 if (!exists("sce_layer")) sce_layer <- fetch_data(type = "sce_layer") -#> 2024-12-12 20:28:09.994977 loading file /github/home/.cache/R/BiocFileCache/5c631378225_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-12-12 20:29:49.567892 loading file /github/home/.cache/R/BiocFileCache/5c84ecba40c_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 9ae63397..ee06e67e 100644 --- a/reference/layer_matrix_plot.html +++ b/reference/layer_matrix_plot.html @@ -20,7 +20,7 @@ spatialLIBD - 1.19.2 + 1.19.3 diff --git a/reference/layer_stat_cor.html b/reference/layer_stat_cor.html index 8d3b48be..925c5b42 100644 --- a/reference/layer_stat_cor.html +++ b/reference/layer_stat_cor.html @@ -17,7 +17,7 @@ spatialLIBD - 1.19.2 + 1.19.3 @@ -161,7 +161,7 @@

Examples

if (!exists("modeling_results")) { modeling_results <- fetch_data(type = "modeling_results") } -#> 2024-12-12 20:28:13.2535 loading file /github/home/.cache/R/BiocFileCache/5c63873b16e_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1 +#> 2024-12-12 20:29:52.499128 loading file /github/home/.cache/R/BiocFileCache/5c8368bad58_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 34920b1b..59f81c7f 100644 --- a/reference/layer_stat_cor_plot.html +++ b/reference/layer_stat_cor_plot.html @@ -22,7 +22,7 @@ spatialLIBD - 1.19.2 + 1.19.3 @@ -169,13 +169,13 @@

Examples

if (!exists("modeling_results")) { modeling_results <- fetch_data(type = "modeling_results") } -#> 2024-12-12 20:28:14.70297 loading file /github/home/.cache/R/BiocFileCache/5c63873b16e_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1 +#> 2024-12-12 20:29:53.559215 loading file /github/home/.cache/R/BiocFileCache/5c8368bad58_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 20:28:15.847515 loading file /github/home/.cache/R/BiocFileCache/104735776034_modeling_results_BayesSpace_k09.Rdata%3Fdl%3D1 +#> 2024-12-12 20:29:54.332465 loading file /github/home/.cache/R/BiocFileCache/1049b69b8d8_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 760f52f4..1b629a14 100644 --- a/reference/libd_layer_colors.html +++ b/reference/libd_layer_colors.html @@ -18,7 +18,7 @@ spatialLIBD - 1.19.2 + 1.19.3 diff --git a/reference/locate_images.html b/reference/locate_images.html index b1ecc16a..dfc7385b 100644 --- a/reference/locate_images.html +++ b/reference/locate_images.html @@ -19,7 +19,7 @@ spatialLIBD - 1.19.2 + 1.19.3 diff --git a/reference/multi_gene_pca.html b/reference/multi_gene_pca.html index 405a64bb..10ea0281 100644 --- a/reference/multi_gene_pca.html +++ b/reference/multi_gene_pca.html @@ -22,7 +22,7 @@ spatialLIBD - 1.19.2 + 1.19.3 diff --git a/reference/multi_gene_sparsity.html b/reference/multi_gene_sparsity.html index db8dd059..db02a67b 100644 --- a/reference/multi_gene_sparsity.html +++ b/reference/multi_gene_sparsity.html @@ -18,7 +18,7 @@ spatialLIBD - 1.19.2 + 1.19.3 diff --git a/reference/multi_gene_z_score.html b/reference/multi_gene_z_score.html index 8be9ac0e..17256e1e 100644 --- a/reference/multi_gene_z_score.html +++ b/reference/multi_gene_z_score.html @@ -18,7 +18,7 @@ spatialLIBD - 1.19.2 + 1.19.3 diff --git a/reference/prep_stitched_data.html b/reference/prep_stitched_data.html index 5e27e99d..3b8690bc 100644 --- a/reference/prep_stitched_data.html +++ b/reference/prep_stitched_data.html @@ -22,7 +22,7 @@ spatialLIBD - 1.19.2 + 1.19.3 diff --git a/reference/read10xVisiumAnalysis.html b/reference/read10xVisiumAnalysis.html index b96b2175..71ff8197 100644 --- a/reference/read10xVisiumAnalysis.html +++ b/reference/read10xVisiumAnalysis.html @@ -18,7 +18,7 @@ spatialLIBD - 1.19.2 + 1.19.3 diff --git a/reference/read10xVisiumWrapper.html b/reference/read10xVisiumWrapper.html index eb68f1db..8b3d6f42 100644 --- a/reference/read10xVisiumWrapper.html +++ b/reference/read10xVisiumWrapper.html @@ -20,7 +20,7 @@ spatialLIBD - 1.19.2 + 1.19.3 diff --git a/reference/registration_block_cor.html b/reference/registration_block_cor.html index 90e45163..2f5f9545 100644 --- a/reference/registration_block_cor.html +++ b/reference/registration_block_cor.html @@ -20,7 +20,7 @@ spatialLIBD - 1.19.2 + 1.19.3 @@ -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 20:28:21.745699 make pseudobulk object -#> 2024-12-12 20:28:21.879578 drop lowly expressed genes -#> 2024-12-12 20:28:21.941366 normalize expression +#> 2024-12-12 20:30:00.262741 make pseudobulk object +#> 2024-12-12 20:30:00.387774 drop lowly expressed genes +#> 2024-12-12 20:30:00.44844 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 20:28:22.020965 create model matrix +#> 2024-12-12 20:30:00.528026 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 20:28:22.03353 run duplicateCorrelation() -#> 2024-12-12 20:28:23.325959 The estimated correlation is: -0.0187869166526901 +#> 2024-12-12 20:30:00.540622 run duplicateCorrelation() +#> 2024-12-12 20:30:01.850952 The estimated correlation is: -0.0187869166526901 diff --git a/reference/registration_model.html b/reference/registration_model.html index 4362df93..2339d21d 100644 --- a/reference/registration_model.html +++ b/reference/registration_model.html @@ -21,7 +21,7 @@ spatialLIBD - 1.19.2 + 1.19.3 @@ -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 20:28:23.635127 make pseudobulk object -#> 2024-12-12 20:28:23.766226 drop lowly expressed genes -#> 2024-12-12 20:28:23.812943 normalize expression +#> 2024-12-12 20:30:02.161799 make pseudobulk object +#> 2024-12-12 20:30:02.292605 drop lowly expressed genes +#> 2024-12-12 20:30:02.339544 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 20:28:23.888787 create model matrix +#> 2024-12-12 20:30:02.415637 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 ae2e7d59..cae2eb72 100644 --- a/reference/registration_pseudobulk.html +++ b/reference/registration_pseudobulk.html @@ -18,7 +18,7 @@ spatialLIBD - 1.19.2 + 1.19.3 @@ -161,9 +161,9 @@

Examples

## Pseudo-bulk sce_pseudo <- registration_pseudobulk(sce, "Cell_Cycle", "sample_id", c("age"), min_ncells = NULL) -#> 2024-12-12 20:28:24.223476 make pseudobulk object -#> 2024-12-12 20:28:24.340239 drop lowly expressed genes -#> 2024-12-12 20:28:24.39338 normalize expression +#> 2024-12-12 20:30:02.740444 make pseudobulk object +#> 2024-12-12 20:30:02.840556 drop lowly expressed genes +#> 2024-12-12 20:30:02.888454 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 ea218541..ed87b955 100644 --- a/reference/registration_stats_anova.html +++ b/reference/registration_stats_anova.html @@ -20,7 +20,7 @@ spatialLIBD - 1.19.2 + 1.19.3 @@ -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 20:28:24.905664 make pseudobulk object -#> 2024-12-12 20:28:25.006561 drop lowly expressed genes -#> 2024-12-12 20:28:25.052977 normalize expression +#> 2024-12-12 20:30:03.407755 make pseudobulk object +#> 2024-12-12 20:30:03.507557 drop lowly expressed genes +#> 2024-12-12 20:30:03.554307 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 20:28:25.128147 create model matrix +#> 2024-12-12 20:30:03.629379 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 20:28:25.13966 run duplicateCorrelation() -#> 2024-12-12 20:28:26.39541 The estimated correlation is: -0.0187869166526901 +#> 2024-12-12 20:30:03.640946 run duplicateCorrelation() +#> 2024-12-12 20:30:04.928178 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 20:28:26.407742 computing F-statistics +#> 2024-12-12 20:30:04.940406 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 20:28:26.469774 computing F-statistics +#> 2024-12-12 20:30:05.001904 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 20:28:26.52057 computing F-statistics +#> 2024-12-12 20:30:05.051664 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 dae997a6..33023ebc 100644 --- a/reference/registration_stats_enrichment.html +++ b/reference/registration_stats_enrichment.html @@ -19,7 +19,7 @@ spatialLIBD - 1.19.2 + 1.19.3 @@ -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 20:28:26.993936 make pseudobulk object -#> 2024-12-12 20:28:27.092498 drop lowly expressed genes -#> 2024-12-12 20:28:27.139499 normalize expression +#> 2024-12-12 20:30:05.52676 make pseudobulk object +#> 2024-12-12 20:30:05.626004 drop lowly expressed genes +#> 2024-12-12 20:30:05.672961 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 20:28:27.214901 create model matrix +#> 2024-12-12 20:30:05.750537 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 20:28:27.226311 run duplicateCorrelation() -#> 2024-12-12 20:28:28.476132 The estimated correlation is: -0.0187869166526901 +#> 2024-12-12 20:30:05.762031 run duplicateCorrelation() +#> 2024-12-12 20:30:07.046864 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 20:28:28.47966 computing enrichment statistics -#> 2024-12-12 20:28:28.5976 extract and reformat enrichment results +#> 2024-12-12 20:30:07.050353 computing enrichment statistics +#> 2024-12-12 20:30:07.167845 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 20:28:28.630564 computing enrichment statistics -#> 2024-12-12 20:28:28.758669 extract and reformat enrichment results +#> 2024-12-12 20:30:07.200581 computing enrichment statistics +#> 2024-12-12 20:30:07.330305 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 4c7c3ace..d33e2ecd 100644 --- a/reference/registration_stats_pairwise.html +++ b/reference/registration_stats_pairwise.html @@ -20,7 +20,7 @@ spatialLIBD - 1.19.2 + 1.19.3 @@ -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 20:28:29.109084 make pseudobulk object -#> 2024-12-12 20:28:29.207035 drop lowly expressed genes -#> 2024-12-12 20:28:29.253472 normalize expression +#> 2024-12-12 20:30:07.686826 make pseudobulk object +#> 2024-12-12 20:30:07.788037 drop lowly expressed genes +#> 2024-12-12 20:30:07.83517 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 20:28:29.327833 create model matrix +#> 2024-12-12 20:30:07.911424 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 20:28:29.339194 run duplicateCorrelation() -#> 2024-12-12 20:28:30.593848 The estimated correlation is: -0.0187869166526901 +#> 2024-12-12 20:30:07.922947 run duplicateCorrelation() +#> 2024-12-12 20:30:09.205465 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 20:28:30.595595 running the baseline pairwise model -#> 2024-12-12 20:28:30.612336 computing pairwise statistics +#> 2024-12-12 20:30:09.207204 running the baseline pairwise model +#> 2024-12-12 20:30:09.223909 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 20:28:30.676997 running the baseline pairwise model -#> 2024-12-12 20:28:30.694467 computing pairwise statistics +#> 2024-12-12 20:30:09.290502 running the baseline pairwise model +#> 2024-12-12 20:30:09.308247 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 41d17482..7bee5387 100644 --- a/reference/registration_wrapper.html +++ b/reference/registration_wrapper.html @@ -22,7 +22,7 @@ spatialLIBD - 1.19.2 + 1.19.3 @@ -207,18 +207,18 @@

Examples

gene_name = "gene_name", suffix = "wrapper" ) -#> 2024-12-12 20:28:31.140335 make pseudobulk object -#> 2024-12-12 20:28:31.237099 dropping 9 pseudo-bulked samples that are below 'min_ncells'. -#> 2024-12-12 20:28:31.250028 drop lowly expressed genes -#> 2024-12-12 20:28:31.29575 normalize expression -#> 2024-12-12 20:28:31.352959 create model matrix -#> 2024-12-12 20:28:31.363419 run duplicateCorrelation() -#> 2024-12-12 20:28:33.747272 The estimated correlation is: -0.0783081238514531 -#> 2024-12-12 20:28:33.749863 computing enrichment statistics -#> 2024-12-12 20:28:33.864692 extract and reformat enrichment results -#> 2024-12-12 20:28:33.890415 running the baseline pairwise model -#> 2024-12-12 20:28:33.908486 computing pairwise statistics -#> 2024-12-12 20:28:33.981533 computing F-statistics +#> 2024-12-12 20:30:09.751545 make pseudobulk object +#> 2024-12-12 20:30:09.850171 dropping 9 pseudo-bulked samples that are below 'min_ncells'. +#> 2024-12-12 20:30:09.863588 drop lowly expressed genes +#> 2024-12-12 20:30:09.910116 normalize expression +#> 2024-12-12 20:30:09.968276 create model matrix +#> 2024-12-12 20:30:09.978954 run duplicateCorrelation() +#> 2024-12-12 20:30:12.42764 The estimated correlation is: -0.0783081238514531 +#> 2024-12-12 20:30:12.430118 computing enrichment statistics +#> 2024-12-12 20:30:12.545472 extract and reformat enrichment results +#> 2024-12-12 20:30:12.571276 running the baseline pairwise model +#> 2024-12-12 20:30:12.589601 computing pairwise statistics +#> 2024-12-12 20:30:12.663869 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 0ce84dde..1f6e5024 100644 --- a/reference/run_app.html +++ b/reference/run_app.html @@ -19,7 +19,7 @@ spatialLIBD - 1.19.2 + 1.19.3 diff --git a/reference/sce_to_spe.html b/reference/sce_to_spe.html index b2817502..47c9bbdb 100644 --- a/reference/sce_to_spe.html +++ b/reference/sce_to_spe.html @@ -21,7 +21,7 @@ spatialLIBD - 1.19.2 + 1.19.3 @@ -127,7 +127,7 @@

Examples

## Transform it to a SpatialExperiment object spe <- sce_to_spe(sce) } -#> 2024-12-12 20:28:36.128955 loading file /github/home/.cache/R/BiocFileCache/104729279b36_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-12-12 20:30:14.247891 loading file /github/home/.cache/R/BiocFileCache/1049eae8491_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 c1090688..e79aa8f4 100644 --- a/reference/sig_genes_extract.html +++ b/reference/sig_genes_extract.html @@ -21,7 +21,7 @@ spatialLIBD - 1.19.2 + 1.19.3 @@ -157,9 +157,9 @@

Examples

if (!exists("modeling_results")) { modeling_results <- fetch_data(type = "modeling_results") } -#> 2024-12-12 20:28:44.616129 loading file /github/home/.cache/R/BiocFileCache/5c63873b16e_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1 +#> 2024-12-12 20:30:22.365428 loading file /github/home/.cache/R/BiocFileCache/5c8368bad58_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1 if (!exists("sce_layer")) sce_layer <- fetch_data(type = "sce_layer") -#> 2024-12-12 20:28:45.768593 loading file /github/home/.cache/R/BiocFileCache/5c631378225_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-12-12 20:30:23.14081 loading file /github/home/.cache/R/BiocFileCache/5c84ecba40c_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 2db0fd6f..6684dd5a 100644 --- a/reference/sig_genes_extract_all.html +++ b/reference/sig_genes_extract_all.html @@ -19,7 +19,7 @@ spatialLIBD - 1.19.2 + 1.19.3 @@ -129,9 +129,9 @@

Examples

if (!exists("modeling_results")) { modeling_results <- fetch_data(type = "modeling_results") } -#> 2024-12-12 20:28:49.033639 loading file /github/home/.cache/R/BiocFileCache/5c63873b16e_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1 +#> 2024-12-12 20:30:26.078694 loading file /github/home/.cache/R/BiocFileCache/5c8368bad58_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1 if (!exists("sce_layer")) sce_layer <- fetch_data(type = "sce_layer") -#> 2024-12-12 20:28:50.142957 loading file /github/home/.cache/R/BiocFileCache/5c631378225_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-12-12 20:30:26.830403 loading file /github/home/.cache/R/BiocFileCache/5c84ecba40c_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 9b755504..1ba00418 100644 --- a/reference/sort_clusters.html +++ b/reference/sort_clusters.html @@ -19,7 +19,7 @@ spatialLIBD - 1.19.2 + 1.19.3 diff --git a/reference/spatialLIBD-package.html b/reference/spatialLIBD-package.html index 07550d21..e0fb0091 100644 --- a/reference/spatialLIBD-package.html +++ b/reference/spatialLIBD-package.html @@ -18,7 +18,7 @@ spatialLIBD - 1.19.2 + 1.19.3 diff --git a/reference/tstats_Human_DLPFC_snRNAseq_Nguyen_topLayer.html b/reference/tstats_Human_DLPFC_snRNAseq_Nguyen_topLayer.html index 84267304..28a5637f 100644 --- a/reference/tstats_Human_DLPFC_snRNAseq_Nguyen_topLayer.html +++ b/reference/tstats_Human_DLPFC_snRNAseq_Nguyen_topLayer.html @@ -23,7 +23,7 @@ spatialLIBD - 1.19.2 + 1.19.3 diff --git a/reference/vis_clus.html b/reference/vis_clus.html index c147dbcb..cb9c7fec 100644 --- a/reference/vis_clus.html +++ b/reference/vis_clus.html @@ -19,7 +19,7 @@ spatialLIBD - 1.19.2 + 1.19.3 @@ -242,7 +242,7 @@

Examples

) print(p4) } -#> 2024-12-12 20:28:52.85705 loading file /github/home/.cache/R/BiocFileCache/104729279b36_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-12-12 20:30:28.966651 loading file /github/home/.cache/R/BiocFileCache/1049eae8491_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 8b1293df..686e40ca 100644 --- a/reference/vis_clus_p.html +++ b/reference/vis_clus_p.html @@ -20,7 +20,7 @@ spatialLIBD - 1.19.2 + 1.19.3 @@ -202,7 +202,7 @@

Examples

## Clean up rm(spe_sub) } -#> 2024-12-12 20:29:05.853802 loading file /github/home/.cache/R/BiocFileCache/104729279b36_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-12-12 20:30:41.566381 loading file /github/home/.cache/R/BiocFileCache/1049eae8491_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 diff --git a/reference/vis_gene.html b/reference/vis_gene.html index b5ffb1ab..77aa145d 100644 --- a/reference/vis_gene.html +++ b/reference/vis_gene.html @@ -20,7 +20,7 @@ spatialLIBD - 1.19.2 + 1.19.3 @@ -341,7 +341,7 @@

Examples

) print(p8) } -#> 2024-12-12 20:29:16.149047 loading file /github/home/.cache/R/BiocFileCache/104729279b36_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-12-12 20:30:51.313372 loading file /github/home/.cache/R/BiocFileCache/1049eae8491_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 aa2b3c87..22fa667f 100644 --- a/reference/vis_gene_p.html +++ b/reference/vis_gene_p.html @@ -21,7 +21,7 @@ spatialLIBD - 1.19.2 + 1.19.3 @@ -215,7 +215,7 @@

Examples

## Clean up rm(spe_sub) } -#> 2024-12-12 20:29:33.927823 loading file /github/home/.cache/R/BiocFileCache/104729279b36_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-12-12 20:31:09.124449 loading file /github/home/.cache/R/BiocFileCache/1049eae8491_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 1060d3a2..217af113 100644 --- a/reference/vis_grid_clus.html +++ b/reference/vis_grid_clus.html @@ -19,7 +19,7 @@ spatialLIBD - 1.19.2 + 1.19.3 @@ -237,7 +237,7 @@

Examples

## for subject 3 cowplot::plot_grid(plotlist = p_list, ncol = 2) } -#> 2024-12-12 20:29:45.056207 loading file /github/home/.cache/R/BiocFileCache/104729279b36_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-12-12 20:31:19.026979 loading file /github/home/.cache/R/BiocFileCache/1049eae8491_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 e9ac0515..73fe713e 100644 --- a/reference/vis_grid_gene.html +++ b/reference/vis_grid_gene.html @@ -20,7 +20,7 @@ spatialLIBD - 1.19.2 + 1.19.3 @@ -256,7 +256,7 @@

Examples

## for subject 3 cowplot::plot_grid(plotlist = p_list, ncol = 2) } -#> 2024-12-12 20:29:56.666488 loading file /github/home/.cache/R/BiocFileCache/104729279b36_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-12-12 20:31:29.819599 loading file /github/home/.cache/R/BiocFileCache/1049eae8491_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1