From 0b1395474ab22e48dc7a8ce84a2bca513d8e1b4d Mon Sep 17 00:00:00 2001 From: lcolladotor Date: Fri, 19 Jul 2024 19:25:32 +0000 Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20LieberIn?= =?UTF-8?q?stitute/spatialLIBD@723cc26af4dcc68475ce6021529ad086856d122f=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 | 2 +- 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 | 4 +-- 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, 207 insertions(+), 207 deletions(-) diff --git a/404.html b/404.html index dcc970a3..df001bac 100644 --- a/404.html +++ b/404.html @@ -40,7 +40,7 @@ spatialLIBD - 1.17.6 + 1.17.7 diff --git a/CODE_OF_CONDUCT.html b/CODE_OF_CONDUCT.html index 18992178..a2aabac0 100644 --- a/CODE_OF_CONDUCT.html +++ b/CODE_OF_CONDUCT.html @@ -17,7 +17,7 @@ spatialLIBD - 1.17.6 + 1.17.7 diff --git a/CONTRIBUTING.html b/CONTRIBUTING.html index 108ead1f..ba14b865 100644 --- a/CONTRIBUTING.html +++ b/CONTRIBUTING.html @@ -17,7 +17,7 @@ spatialLIBD - 1.17.6 + 1.17.7 diff --git a/SUPPORT.html b/SUPPORT.html index d55046f9..14425a1d 100644 --- a/SUPPORT.html +++ b/SUPPORT.html @@ -17,7 +17,7 @@ spatialLIBD - 1.17.6 + 1.17.7 diff --git a/articles/TenX_data_download.html b/articles/TenX_data_download.html index 0f30d9cd..e67b3fd9 100644 --- a/articles/TenX_data_download.html +++ b/articles/TenX_data_download.html @@ -39,7 +39,7 @@ spatialLIBD - 1.17.6 + 1.17.7 @@ -532,7 +532,7 @@

From Gencode## Show the GTF cache location gtf_cache #> BFC4 -#> "/github/home/.cache/R/BiocFileCache/29a6988c8e0_gencode.v32.annotation.gtf.gz" +#> "/github/home/.cache/R/BiocFileCache/2e225d89478_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 ) -#> 2024-07-19 16:19:02.753467 SpatialExperiment::read10xVisium: reading basic data from SpaceRanger -#> 2024-07-19 16:19:14.217134 read10xVisiumAnalysis: reading analysis output from SpaceRanger -#> 2024-07-19 16:19:14.32263 add10xVisiumAnalysis: adding analysis output from SpaceRanger -#> 2024-07-19 16:19:14.568816 rtracklayer::import: reading the reference GTF file -#> 2024-07-19 16:19:42.783317 adding gene information to the SPE object +#> 2024-07-19 19:24:36.404432 SpatialExperiment::read10xVisium: reading basic data from SpaceRanger +#> 2024-07-19 19:24:48.034181 read10xVisiumAnalysis: reading analysis output from SpaceRanger +#> 2024-07-19 19:24:48.141866 add10xVisiumAnalysis: adding analysis output from SpaceRanger +#> 2024-07-19 19:24:48.389162 rtracklayer::import: reading the reference GTF file +#> 2024-07-19 19:25:16.045896 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. -#> 2024-07-19 16:19:43.044241 adding information used by spatialLIBD +#> 2024-07-19 19:25:16.328508 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] "2024-07-19 16:19:44 UTC"
+
#> [1] "2024-07-19 19:25:17 UTC"

Wallclock time spent generating the vignette.

-
#> Time difference of 1.719 mins
+
#> Time difference of 1.717 mins

R session information.

#> ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
 #>  setting  value
@@ -1281,7 +1281,7 @@ 
Reproducibility#>  SparseArray            1.4.8     2024-05-24 [1] Bioconductor 3.19 (R 4.4.1)
 #>  sparseMatrixStats      1.16.0    2024-04-30 [1] Bioconductor 3.19 (R 4.4.1)
 #>  SpatialExperiment    * 1.14.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.1)
-#>  spatialLIBD          * 1.17.6    2024-07-19 [1] Bioconductor
+#>  spatialLIBD          * 1.17.7    2024-07-19 [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 d94b7252..3be3820b 100644
--- a/articles/guide_to_spatial_registration.html
+++ b/articles/guide_to_spatial_registration.html
@@ -39,7 +39,7 @@
       
       
         spatialLIBD
-        1.17.6
+        1.17.7
       
     
 
@@ -288,7 +288,7 @@ 
Spatial Reference
 ## get reference layer enrichment statistics
 layer_modeling_results <- fetch_data(type = "modeling_results")
-#> 2024-07-19 16:16:00.611289 loading file /github/home/.cache/R/BiocFileCache/29a61439eba_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
+#> 2024-07-19 19:21:39.259184 loading file /github/home/.cache/R/BiocFileCache/2e21996cc5_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"
 )
-#> 2024-07-19 16:16:08.538015 make pseudobulk object
-#> 2024-07-19 16:16:10.258196 dropping 13 pseudo-bulked samples that are below 'min_ncells'.
-#> 2024-07-19 16:16:10.320936 drop lowly expressed genes
-#> 2024-07-19 16:16:10.490465 normalize expression
-#> 2024-07-19 16:16:12.000376 create model matrix
-#> 2024-07-19 16:16:12.023942 run duplicateCorrelation()
-#> 2024-07-19 16:16:25.396277 The estimated correlation is: 0.138734774807097
-#> 2024-07-19 16:16:25.398754 computing enrichment statistics
-#> 2024-07-19 16:16:26.54759 extract and reformat enrichment results
-#> 2024-07-19 16:16:26.604601 running the baseline pairwise model
-#> 2024-07-19 16:16:26.77372 computing pairwise statistics
-#> 2024-07-19 16:16:28.127121 computing F-statistics

+#> 2024-07-19 19:21:47.076811 make pseudobulk object
+#> 2024-07-19 19:21:48.863408 dropping 13 pseudo-bulked samples that are below 'min_ncells'.
+#> 2024-07-19 19:21:48.936572 drop lowly expressed genes
+#> 2024-07-19 19:21:49.107141 normalize expression
+#> 2024-07-19 19:21:50.60615 create model matrix
+#> 2024-07-19 19:21:50.629522 run duplicateCorrelation()
+#> 2024-07-19 19:22:03.71682 The estimated correlation is: 0.138734774807097
+#> 2024-07-19 19:22:03.719387 computing enrichment statistics
+#> 2024-07-19 19:22:04.841307 extract and reformat enrichment results
+#> 2024-07-19 19:22:04.932997 running the baseline pairwise model
+#> 2024-07-19 19:22:05.108508 computing pairwise statistics
+#> 2024-07-19 19:22:06.452383 computing F-statistics

Extract Enrichment t-statistics @@ -562,9 +562,9 @@

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

Date the vignette was generated.

-
#> [1] "2024-07-19 16:16:29 UTC"
+
#> [1] "2024-07-19 19:22:07 UTC"

Wallclock time spent generating the vignette.

-
#> Time difference of 42.309 secs
+
#> Time difference of 41.203 secs

R session information.

#> ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
 #>  setting  value
@@ -716,7 +716,7 @@ 
Reproducibility#>  SparseArray            1.4.8     2024-05-24 [1] Bioconductor 3.19 (R 4.4.1)
 #>  sparseMatrixStats      1.16.0    2024-04-30 [1] Bioconductor 3.19 (R 4.4.1)
 #>  SpatialExperiment    * 1.14.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.1)
-#>  spatialLIBD          * 1.17.6    2024-07-19 [1] Bioconductor
+#>  spatialLIBD          * 1.17.7    2024-07-19 [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 374c6159..b91ce2c1 100644
--- a/articles/index.html
+++ b/articles/index.html
@@ -17,7 +17,7 @@
       
       
         spatialLIBD
-        1.17.6
+        1.17.7
       
     
 
diff --git a/articles/multi_gene_plots.html b/articles/multi_gene_plots.html
index d257830e..dfb59adf 100644
--- a/articles/multi_gene_plots.html
+++ b/articles/multi_gene_plots.html
@@ -39,7 +39,7 @@
       
       
         spatialLIBD
-        1.17.6
+        1.17.7
       
     
 
@@ -195,9 +195,9 @@ 
Plotting One Gene
 modeling_results <- fetch_data(type = "modeling_results")
-#> 2024-07-19 16:16:56.883392 loading file /github/home/.cache/R/BiocFileCache/29a61439eba_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
+#> 2024-07-19 19:22:33.566292 loading file /github/home/.cache/R/BiocFileCache/2e21996cc5_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
 sce_layer <- fetch_data(type = "sce_layer")
-#> 2024-07-19 16:16:58.160597 loading file /github/home/.cache/R/BiocFileCache/29a7aca31b5_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-07-19 19:22:34.584327 loading file /github/home/.cache/R/BiocFileCache/2e2552c8efc_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] "2024-07-19 16:17:14 UTC"

+
#> [1] "2024-07-19 19:22:50 UTC"

 
Wallclock time spent generating the vignette.

-
#> Time difference of 39.001 secs

+
#> Time difference of 37.506 secs

 
R session information.

 
#> ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
 #>  setting  value
@@ -577,7 +577,7 @@ 
Reproducibility#>  SparseArray            1.4.8     2024-05-24 [1] Bioconductor 3.19 (R 4.4.1)
 #>  sparseMatrixStats      1.16.0    2024-04-30 [1] Bioconductor 3.19 (R 4.4.1)
 #>  SpatialExperiment    * 1.14.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.1)
-#>  spatialLIBD          * 1.17.6    2024-07-19 [1] Bioconductor
+#>  spatialLIBD          * 1.17.7    2024-07-19 [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 a2718562..7e234633 100644
--- a/articles/spatialLIBD.html
+++ b/articles/spatialLIBD.html
@@ -39,7 +39,7 @@
       
       
         spatialLIBD
-        1.17.6
+        1.17.7
       
     
 
@@ -414,7 +414,7 @@ 
Downloading the data with s
 
 ## Download the small example sce data
 sce <- fetch_data(type = "sce_example", eh = ehub)
-#> 2024-07-19 16:17:31.559991 loading file /github/home/.cache/R/BiocFileCache/29a884cc23_sce_sub_for_vignette.Rdata%3Fdl%3D1
+#> 2024-07-19 19:23:07.278777 loading file /github/home/.cache/R/BiocFileCache/2e255dd2a6d_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)
-#> 2024-07-19 16:17:38.042387 loading file /github/home/.cache/R/BiocFileCache/29a7aca31b5_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-07-19 19:23:11.653191 loading file /github/home/.cache/R/BiocFileCache/2e2552c8efc_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
 modeling_results <- fetch_data("modeling_results", eh = ehub)
-#> 2024-07-19 16:17:38.492312 loading file /github/home/.cache/R/BiocFileCache/29a61439eba_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1

+#> 2024-07-19 19:23:12.098435 loading file /github/home/.cache/R/BiocFileCache/2e21996cc5_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 
-#>  10.125   0.316  10.461
+#>  10.024   0.360  10.398
 
 ## Explore the result
 class(sig_genes)
@@ -1377,9 +1377,9 @@ 
Reproducibilitylibrary("knitr")
 knit("spatialLIBD.Rmd", tangle = TRUE)

 
Date the vignette was generated.

-
#> [1] "2024-07-19 16:17:56 UTC"

+
#> [1] "2024-07-19 19:23:29 UTC"

 
Wallclock time spent generating the vignette.

-
#> Time difference of 38.179 secs

+
#> Time difference of 35.597 secs

 
R session information.

 
#> ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
 #>  setting  value
@@ -1533,7 +1533,7 @@ 
Reproducibility#>  SparseArray            1.4.8     2024-05-24 [1] Bioconductor 3.19 (R 4.4.1)
 #>  sparseMatrixStats      1.16.0    2024-04-30 [1] Bioconductor 3.19 (R 4.4.1)
 #>  SpatialExperiment    * 1.14.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.1)
-#>  spatialLIBD          * 1.17.6    2024-07-19 [1] Bioconductor
+#>  spatialLIBD          * 1.17.7    2024-07-19 [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 5953cb2d..0f46c337 100644
--- a/authors.html
+++ b/authors.html
@@ -17,7 +17,7 @@
       
       
         spatialLIBD
-        1.17.6
+        1.17.7
       
     
 
diff --git a/index.html b/index.html
index 47718271..482941cc 100644
--- a/index.html
+++ b/index.html
@@ -41,7 +41,7 @@
       
       
         spatialLIBD
-        1.17.6
+        1.17.7
       
     
 
diff --git a/news/index.html b/news/index.html
index 93a36916..75bf95d5 100644
--- a/news/index.html
+++ b/news/index.html
@@ -17,7 +17,7 @@
       
       
         spatialLIBD
-        1.17.6
+        1.17.7
       
     
 
diff --git a/pkgdown.yml b/pkgdown.yml
index 1e1566e3..d7fdecb4 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: 2024-07-19T16:09Z
+last_built: 2024-07-19T19:15Z
diff --git a/reference/add10xVisiumAnalysis.html b/reference/add10xVisiumAnalysis.html
index 6dd8b9b8..f33e153c 100644
--- a/reference/add10xVisiumAnalysis.html
+++ b/reference/add10xVisiumAnalysis.html
@@ -19,7 +19,7 @@
       
       
         spatialLIBD
-        1.17.6
+        1.17.7
       
     
 
diff --git a/reference/add_images.html b/reference/add_images.html
index 941cf2a5..8789d4ff 100644
--- a/reference/add_images.html
+++ b/reference/add_images.html
@@ -25,7 +25,7 @@
       
       
         spatialLIBD
-        1.17.6
+        1.17.7
       
     
 
@@ -165,29 +165,29 @@ 
Examples

         image_paths = c("151507" = "https://spatial-dlpfc.s3.us-east-2.amazonaws.com/images/151507_tissue_lowres_image.png")
     ))
 }
-#> 2024-07-19 16:09:52.138447 loading file /github/home/.cache/R/BiocFileCache/d681608cce0_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
-#> 2024-07-19 16:10:07.79198 adding image for sample 151507
-#> 2024-07-19 16:10:09.418116 adding image for sample 151508
+#> 2024-07-19 19:15:52.227992 loading file /github/home/.cache/R/BiocFileCache/db1206d4b6_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-07-19 19:16:07.668686 adding image for sample 151507
+#> 2024-07-19 19:16:08.45512 adding image for sample 151508
 #> Warning: No image was found for sample: 151508
-#> 2024-07-19 16:10:09.418445 adding image for sample 151509
+#> 2024-07-19 19:16:08.455442 adding image for sample 151509
 #> Warning: No image was found for sample: 151509
-#> 2024-07-19 16:10:09.418663 adding image for sample 151510
+#> 2024-07-19 19:16:08.455653 adding image for sample 151510
 #> Warning: No image was found for sample: 151510
-#> 2024-07-19 16:10:09.418864 adding image for sample 151669
+#> 2024-07-19 19:16:08.455849 adding image for sample 151669
 #> Warning: No image was found for sample: 151669
-#> 2024-07-19 16:10:09.419069 adding image for sample 151670
+#> 2024-07-19 19:16:08.456042 adding image for sample 151670
 #> Warning: No image was found for sample: 151670
-#> 2024-07-19 16:10:09.419261 adding image for sample 151671
+#> 2024-07-19 19:16:08.456234 adding image for sample 151671
 #> Warning: No image was found for sample: 151671
-#> 2024-07-19 16:10:09.419522 adding image for sample 151672
+#> 2024-07-19 19:16:08.45645 adding image for sample 151672
 #> Warning: No image was found for sample: 151672
-#> 2024-07-19 16:10:09.419721 adding image for sample 151673
+#> 2024-07-19 19:16:08.456644 adding image for sample 151673
 #> Warning: No image was found for sample: 151673
-#> 2024-07-19 16:10:09.419913 adding image for sample 151674
+#> 2024-07-19 19:16:08.456837 adding image for sample 151674
 #> Warning: No image was found for sample: 151674
-#> 2024-07-19 16:10:09.420102 adding image for sample 151675
+#> 2024-07-19 19:16:08.457031 adding image for sample 151675
 #> Warning: No image was found for sample: 151675
-#> 2024-07-19 16:10:09.420296 adding image for sample 151676
+#> 2024-07-19 19:16:08.457219 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 bdd350e8..29ae78ee 100644
--- a/reference/add_key.html
+++ b/reference/add_key.html
@@ -19,7 +19,7 @@
       
       
         spatialLIBD
-        1.17.6
+        1.17.7
       
     
 
@@ -124,7 +124,7 @@ 
Examples

     spe$key_original <- NULL
     head(spe$key)
 }
-#> 2024-07-19 16:10:12.307687 loading file /github/home/.cache/R/BiocFileCache/d681608cce0_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-07-19 19:16:10.842579 loading file /github/home/.cache/R/BiocFileCache/db1206d4b6_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 25305d69..9fa83c2e 100644
--- a/reference/add_qc_metrics.html
+++ b/reference/add_qc_metrics.html
@@ -21,7 +21,7 @@
       
       
         spatialLIBD
-        1.17.6
+        1.17.7
       
     
 
@@ -144,7 +144,7 @@ 
Author

     
Examples

     
## Obtain the necessary data
 spe_pre_qc <- fetch_data("spatialDLPFC_Visium_example_subset")
-#> 2024-07-19 16:10:28.484995 loading file /github/home/.cache/R/BiocFileCache/29a3d048335_spatialDLPFC_spe_subset_example.rds%3Fdl%3D1
+#> 2024-07-19 19:16:26.317369 loading file /github/home/.cache/R/BiocFileCache/2e224b1c08a_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 4b1ef65a..613df2b8 100644
--- a/reference/annotate_registered_clusters.html
+++ b/reference/annotate_registered_clusters.html
@@ -21,7 +21,7 @@
       
       
         spatialLIBD
-        1.17.6
+        1.17.7
       
     

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

 if (!exists("modeling_results")) {
     modeling_results <- fetch_data(type = "modeling_results")
 }
-#> 2024-07-19 16:10:41.818557 loading file /github/home/.cache/R/BiocFileCache/29a61439eba_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
+#> 2024-07-19 19:16:38.976183 loading file /github/home/.cache/R/BiocFileCache/2e21996cc5_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 3291c005..b627b15f 100644
--- a/reference/check_modeling_results.html
+++ b/reference/check_modeling_results.html
@@ -18,7 +18,7 @@
       
       
         spatialLIBD
-        1.17.6
+        1.17.7
       
     
 
@@ -108,7 +108,7 @@ 
Examples

 if (!exists("modeling_results")) {
     modeling_results <- fetch_data(type = "modeling_results")
 }
-#> 2024-07-19 16:10:43.258538 loading file /github/home/.cache/R/BiocFileCache/29a61439eba_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
+#> 2024-07-19 19:16:40.102475 loading file /github/home/.cache/R/BiocFileCache/2e21996cc5_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 47c6bdd4..94921783 100644
--- a/reference/check_sce.html
+++ b/reference/check_sce.html
@@ -20,7 +20,7 @@
       
       
         spatialLIBD
-        1.17.6
+        1.17.7
       
     
 
@@ -131,7 +131,7 @@ 
Examples

     ## Check the object
     check_sce(sce_example)
 }
-#> 2024-07-19 16:10:44.713817 loading file /github/home/.cache/R/BiocFileCache/29a884cc23_sce_sub_for_vignette.Rdata%3Fdl%3D1
+#> 2024-07-19 19:16:41.196573 loading file /github/home/.cache/R/BiocFileCache/2e255dd2a6d_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 74decede..97d0fed9 100644
--- a/reference/check_sce_layer.html
+++ b/reference/check_sce_layer.html
@@ -18,7 +18,7 @@
       
       
         spatialLIBD
-        1.17.6
+        1.17.7
       
     
 
@@ -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")
-#> 2024-07-19 16:10:47.459765 loading file /github/home/.cache/R/BiocFileCache/29a7aca31b5_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-07-19 19:16:43.59675 loading file /github/home/.cache/R/BiocFileCache/2e2552c8efc_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 bcdbd2c4..12cf37d4 100644
--- a/reference/check_spe.html
+++ b/reference/check_spe.html
@@ -18,7 +18,7 @@
       
       
         spatialLIBD
-        1.17.6
+        1.17.7
       
     
 
@@ -123,7 +123,7 @@ 
Examples

     ## Check the object
     check_spe(spe)
 }
-#> 2024-07-19 16:10:49.005781 loading file /github/home/.cache/R/BiocFileCache/d681608cce0_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-07-19 19:16:44.784084 loading file /github/home/.cache/R/BiocFileCache/db1206d4b6_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 6b086ff7..4c5ff3a4 100644
--- a/reference/cluster_export.html
+++ b/reference/cluster_export.html
@@ -21,7 +21,7 @@
       
       
         spatialLIBD
-        1.17.6
+        1.17.7
       
     
 
@@ -134,7 +134,7 @@ 
Examples

     cluster_export(spe, "spatialLIBD")
     cluster_export(spe, "GraphBased")
 }
-#> 2024-07-19 16:11:04.182544 loading file /github/home/.cache/R/BiocFileCache/d681608cce0_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-07-19 19:16:59.384119 loading file /github/home/.cache/R/BiocFileCache/db1206d4b6_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 77194085..9289c9ed 100644
--- a/reference/cluster_import.html
+++ b/reference/cluster_import.html
@@ -20,7 +20,7 @@
       
       
         spatialLIBD
-        1.17.6
+        1.17.7
       
     
 
@@ -137,11 +137,11 @@ 
Examples

     ## Re-import them
     colData(cluster_import(spe))
 }
-#> 2024-07-19 16:11:20.175964 loading file /github/home/.cache/R/BiocFileCache/d681608cce0_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-07-19 19:17:14.468768 loading file /github/home/.cache/R/BiocFileCache/db1206d4b6_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
 #> Overwriting 'spe$key'. Set 'overwrite = FALSE' if you do not want to overwrite it.
-#> Warning: '/tmp/RtmpB9bykw/exported_clusters/spatialLIBD' already exists
+#> Warning: '/tmp/RtmpKFVgjO/exported_clusters/spatialLIBD' already exists
 #> Overwriting 'spe$key'. Set 'overwrite = FALSE' if you do not want to overwrite it.
-#> Warning: '/tmp/RtmpB9bykw/exported_clusters/GraphBased' already exists
+#> Warning: '/tmp/RtmpKFVgjO/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 17fada89..e8054fff 100644
--- a/reference/enough_ram.html
+++ b/reference/enough_ram.html
@@ -17,7 +17,7 @@
       
       
         spatialLIBD
-        1.17.6
+        1.17.7
       
     
 
diff --git a/reference/fetch_data.html b/reference/fetch_data.html
index e2dc764d..b3834137 100644
--- a/reference/fetch_data.html
+++ b/reference/fetch_data.html
@@ -25,7 +25,7 @@
       
       
         spatialLIBD
-        1.17.6
+        1.17.7
       
     
 
@@ -166,7 +166,7 @@ 
Examples

 ## Download the SingleCellExperiment object
 ## at the layer-level
 if (!exists("sce_layer")) sce_layer <- fetch_data("sce_layer")
-#> 2024-07-19 16:11:36.412115 loading file /github/home/.cache/R/BiocFileCache/29a7aca31b5_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-07-19 19:17:29.707474 loading file /github/home/.cache/R/BiocFileCache/2e2552c8efc_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 39e480ec..ea22fb15 100644
--- a/reference/frame_limits.html
+++ b/reference/frame_limits.html
@@ -27,7 +27,7 @@
       
       
         spatialLIBD
-        1.17.6
+        1.17.7
       
     
 
@@ -154,7 +154,7 @@ 
Examples

     ## Obtain the frame limits for one sample
     frame_limits(spe, sampleid = "151673")
 }
-#> 2024-07-19 16:11:39.43027 loading file /github/home/.cache/R/BiocFileCache/d681608cce0_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-07-19 19:17:32.277201 loading file /github/home/.cache/R/BiocFileCache/db1206d4b6_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 d3e8510b..20c8c1e9 100644
--- a/reference/gene_set_enrichment.html
+++ b/reference/gene_set_enrichment.html
@@ -22,7 +22,7 @@
       
       
         spatialLIBD
-        1.17.6
+        1.17.7
       
     
 
@@ -176,7 +176,7 @@ 
Examples

 if (!exists("modeling_results")) {
     modeling_results <- fetch_data(type = "modeling_results")
 }
-#> 2024-07-19 16:11:54.097397 loading file /github/home/.cache/R/BiocFileCache/29a61439eba_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
+#> 2024-07-19 19:17:46.383027 loading file /github/home/.cache/R/BiocFileCache/2e21996cc5_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 740fda1c..5fc60a67 100644
--- a/reference/gene_set_enrichment_plot.html
+++ b/reference/gene_set_enrichment_plot.html
@@ -18,7 +18,7 @@
       
       
         spatialLIBD
-        1.17.6
+        1.17.7
       
     
 
@@ -178,7 +178,7 @@ 
Examples

 if (!exists("modeling_results")) {
     modeling_results <- fetch_data(type = "modeling_results")
 }
-#> 2024-07-19 16:11:55.800884 loading file /github/home/.cache/R/BiocFileCache/29a61439eba_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
+#> 2024-07-19 19:17:47.893005 loading file /github/home/.cache/R/BiocFileCache/2e21996cc5_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 f891c8d3..bf75553e 100644
--- a/reference/geom_spatial.html
+++ b/reference/geom_spatial.html
@@ -20,7 +20,7 @@
       
       
         spatialLIBD
-        1.17.6
+        1.17.7
       
     
 
@@ -175,7 +175,7 @@ 
Examples

     ## Clean up
     rm(spe_sub)
 }
-#> 2024-07-19 16:11:58.001161 loading file /github/home/.cache/R/BiocFileCache/d681608cce0_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-07-19 19:17:49.787475 loading file /github/home/.cache/R/BiocFileCache/db1206d4b6_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
diff --git a/reference/get_colors.html b/reference/get_colors.html index f57d0ac9..1f521582 100644 --- a/reference/get_colors.html +++ b/reference/get_colors.html @@ -18,7 +18,7 @@ spatialLIBD - 1.17.6 + 1.17.7 @@ -105,7 +105,7 @@

Examples


 ## Obtain the necessary data
 if (!exists("sce_layer")) sce_layer <- fetch_data("sce_layer")
-#> 2024-07-19 16:12:15.87135 loading file /github/home/.cache/R/BiocFileCache/29a7aca31b5_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-07-19 19:18:05.181893 loading file /github/home/.cache/R/BiocFileCache/2e2552c8efc_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 f90dd515..a2e57592 100644
--- a/reference/img_edit.html
+++ b/reference/img_edit.html
@@ -19,7 +19,7 @@
       
       
         spatialLIBD
-        1.17.6
+        1.17.7
@@ -222,7 +222,7 @@

Examples

x <- img_edit(spe, sampleid = "151507", brightness = 25) plot(x) } -#> 2024-07-19 16:12:17.438233 loading file /github/home/.cache/R/BiocFileCache/d681608cce0_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-07-19 19:18:06.487716 loading file /github/home/.cache/R/BiocFileCache/db1206d4b6_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 diff --git a/reference/img_update.html b/reference/img_update.html index 3a376265..0f82f96c 100644 --- a/reference/img_update.html +++ b/reference/img_update.html @@ -17,7 +17,7 @@ spatialLIBD - 1.17.6 + 1.17.7 @@ -139,7 +139,7 @@

Examples

## Reduce brightness to 25% and update the imgData() imgData(img_update(spe, sampleid = "151507", brightness = 25)) } -#> 2024-07-19 16:12:33.778756 loading file /github/home/.cache/R/BiocFileCache/d681608cce0_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-07-19 19:18:21.95952 loading file /github/home/.cache/R/BiocFileCache/db1206d4b6_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 bb9b1338..154841f8 100644 --- a/reference/img_update_all.html +++ b/reference/img_update_all.html @@ -19,7 +19,7 @@ spatialLIBD - 1.17.6 + 1.17.7 @@ -138,7 +138,7 @@

Examples

## update the imgData() imgData(img_update_all(spe, brightness = 25)) } -#> 2024-07-19 16:12:48.567655 loading file /github/home/.cache/R/BiocFileCache/d681608cce0_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-07-19 19:18:36.137008 loading file /github/home/.cache/R/BiocFileCache/db1206d4b6_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 fdcce2ae..d7f7deba 100644 --- a/reference/index.html +++ b/reference/index.html @@ -17,7 +17,7 @@ spatialLIBD - 1.17.6 + 1.17.7 diff --git a/reference/layer_boxplot.html b/reference/layer_boxplot.html index ba48adb0..784e062d 100644 --- a/reference/layer_boxplot.html +++ b/reference/layer_boxplot.html @@ -19,7 +19,7 @@ spatialLIBD - 1.17.6 + 1.17.7 @@ -185,9 +185,9 @@

Examples

if (!exists("modeling_results")) { modeling_results <- fetch_data(type = "modeling_results") } -#> 2024-07-19 16:13:06.23228 loading file /github/home/.cache/R/BiocFileCache/29a61439eba_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1 +#> 2024-07-19 19:18:53.631853 loading file /github/home/.cache/R/BiocFileCache/2e21996cc5_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1 if (!exists("sce_layer")) sce_layer <- fetch_data(type = "sce_layer") -#> 2024-07-19 16:13:07.455083 loading file /github/home/.cache/R/BiocFileCache/29a7aca31b5_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-07-19 19:18:54.578097 loading file /github/home/.cache/R/BiocFileCache/2e2552c8efc_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 d5cd6750..30c3ef22 100644 --- a/reference/layer_matrix_plot.html +++ b/reference/layer_matrix_plot.html @@ -20,7 +20,7 @@ spatialLIBD - 1.17.6 + 1.17.7 diff --git a/reference/layer_stat_cor.html b/reference/layer_stat_cor.html index fd4634e8..3d1c58d9 100644 --- a/reference/layer_stat_cor.html +++ b/reference/layer_stat_cor.html @@ -17,7 +17,7 @@ spatialLIBD - 1.17.6 + 1.17.7 @@ -156,7 +156,7 @@

Examples

if (!exists("modeling_results")) { modeling_results <- fetch_data(type = "modeling_results") } -#> 2024-07-19 16:13:11.48902 loading file /github/home/.cache/R/BiocFileCache/29a61439eba_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1 +#> 2024-07-19 19:18:58.028239 loading file /github/home/.cache/R/BiocFileCache/2e21996cc5_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 99c22980..b574a47d 100644 --- a/reference/layer_stat_cor_plot.html +++ b/reference/layer_stat_cor_plot.html @@ -20,7 +20,7 @@ spatialLIBD - 1.17.6 + 1.17.7 @@ -145,7 +145,7 @@

Examples

if (!exists("modeling_results")) { modeling_results <- fetch_data(type = "modeling_results") } -#> 2024-07-19 16:13:12.982246 loading file /github/home/.cache/R/BiocFileCache/29a61439eba_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1 +#> 2024-07-19 19:18:59.162965 loading file /github/home/.cache/R/BiocFileCache/2e21996cc5_Human_DLPFC_Visium_modeling_results.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 6a843fec..9cd2885c 100644 --- a/reference/libd_layer_colors.html +++ b/reference/libd_layer_colors.html @@ -18,7 +18,7 @@ spatialLIBD - 1.17.6 + 1.17.7 diff --git a/reference/locate_images.html b/reference/locate_images.html index 8cbe293c..d27b7709 100644 --- a/reference/locate_images.html +++ b/reference/locate_images.html @@ -19,7 +19,7 @@ spatialLIBD - 1.17.6 + 1.17.7 diff --git a/reference/multi_gene_pca.html b/reference/multi_gene_pca.html index 334fbe7d..8d5d99c7 100644 --- a/reference/multi_gene_pca.html +++ b/reference/multi_gene_pca.html @@ -22,7 +22,7 @@ spatialLIBD - 1.17.6 + 1.17.7 diff --git a/reference/multi_gene_sparsity.html b/reference/multi_gene_sparsity.html index 2ababa43..261a3a9e 100644 --- a/reference/multi_gene_sparsity.html +++ b/reference/multi_gene_sparsity.html @@ -18,7 +18,7 @@ spatialLIBD - 1.17.6 + 1.17.7 diff --git a/reference/multi_gene_z_score.html b/reference/multi_gene_z_score.html index ce8a878a..d196615d 100644 --- a/reference/multi_gene_z_score.html +++ b/reference/multi_gene_z_score.html @@ -18,7 +18,7 @@ spatialLIBD - 1.17.6 + 1.17.7 diff --git a/reference/prep_stitched_data.html b/reference/prep_stitched_data.html index 36678e3a..4ac1081c 100644 --- a/reference/prep_stitched_data.html +++ b/reference/prep_stitched_data.html @@ -22,7 +22,7 @@ spatialLIBD - 1.17.6 + 1.17.7 diff --git a/reference/read10xVisiumAnalysis.html b/reference/read10xVisiumAnalysis.html index 7e04bd5b..197d5722 100644 --- a/reference/read10xVisiumAnalysis.html +++ b/reference/read10xVisiumAnalysis.html @@ -18,7 +18,7 @@ spatialLIBD - 1.17.6 + 1.17.7 diff --git a/reference/read10xVisiumWrapper.html b/reference/read10xVisiumWrapper.html index c8d01991..b377a0b1 100644 --- a/reference/read10xVisiumWrapper.html +++ b/reference/read10xVisiumWrapper.html @@ -20,7 +20,7 @@ spatialLIBD - 1.17.6 + 1.17.7 diff --git a/reference/registration_block_cor.html b/reference/registration_block_cor.html index 4e9588d2..d4076bf6 100644 --- a/reference/registration_block_cor.html +++ b/reference/registration_block_cor.html @@ -20,7 +20,7 @@ spatialLIBD - 1.17.6 + 1.17.7 @@ -146,9 +146,9 @@

Examples

#> #> rgstr_> ## Pseudo-bulk #> rgstr_> sce_pseudo <- registration_pseudobulk(sce, "Cell_Cycle", "sample_id", c("age"), min_ncells = NULL) -#> 2024-07-19 16:13:16.270864 make pseudobulk object -#> 2024-07-19 16:13:16.474003 drop lowly expressed genes -#> 2024-07-19 16:13:16.546143 normalize expression +#> 2024-07-19 19:19:02.478811 make pseudobulk object +#> 2024-07-19 19:19:02.665889 drop lowly expressed genes +#> 2024-07-19 19:19:02.739875 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") -#> 2024-07-19 16:13:16.62635 create model matrix +#> 2024-07-19 19:19:02.819938 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) -#> 2024-07-19 16:13:16.639346 run duplicateCorrelation() -#> 2024-07-19 16:13:17.929264 The estimated correlation is: -0.0187869166526901 +#> 2024-07-19 19:19:02.832737 run duplicateCorrelation() +#> 2024-07-19 19:19:04.09376 The estimated correlation is: -0.0187869166526901 diff --git a/reference/registration_model.html b/reference/registration_model.html index 24da77d5..fd2825e9 100644 --- a/reference/registration_model.html +++ b/reference/registration_model.html @@ -21,7 +21,7 @@ spatialLIBD - 1.17.6 + 1.17.7 @@ -148,9 +148,9 @@

Examples

#> #> rgstr_> ## Pseudo-bulk #> rgstr_> sce_pseudo <- registration_pseudobulk(sce, "Cell_Cycle", "sample_id", c("age"), min_ncells = NULL) -#> 2024-07-19 16:13:18.385009 make pseudobulk object -#> 2024-07-19 16:13:18.576205 drop lowly expressed genes -#> 2024-07-19 16:13:18.632249 normalize expression +#> 2024-07-19 19:19:04.539991 make pseudobulk object +#> 2024-07-19 19:19:04.731875 drop lowly expressed genes +#> 2024-07-19 19:19:04.786694 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") -#> 2024-07-19 16:13:18.70822 create model matrix +#> 2024-07-19 19:19:04.861596 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 91591ced..ab80232c 100644 --- a/reference/registration_pseudobulk.html +++ b/reference/registration_pseudobulk.html @@ -18,7 +18,7 @@ spatialLIBD - 1.17.6 + 1.17.7 @@ -159,9 +159,9 @@

Examples

## Pseudo-bulk sce_pseudo <- registration_pseudobulk(sce, "Cell_Cycle", "sample_id", c("age"), min_ncells = NULL) -#> 2024-07-19 16:13:19.179466 make pseudobulk object -#> 2024-07-19 16:13:19.336172 drop lowly expressed genes -#> 2024-07-19 16:13:19.393149 normalize expression +#> 2024-07-19 19:19:05.326214 make pseudobulk object +#> 2024-07-19 19:19:05.48246 drop lowly expressed genes +#> 2024-07-19 19:19:05.536866 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 360bed9c..eabccff7 100644 --- a/reference/registration_stats_anova.html +++ b/reference/registration_stats_anova.html @@ -20,7 +20,7 @@ spatialLIBD - 1.17.6 + 1.17.7 @@ -180,9 +180,9 @@

Examples

#> #> rgstr_> ## Pseudo-bulk #> rgstr_> sce_pseudo <- registration_pseudobulk(sce, "Cell_Cycle", "sample_id", c("age"), min_ncells = NULL) -#> 2024-07-19 16:13:20.009561 make pseudobulk object -#> 2024-07-19 16:13:20.198606 drop lowly expressed genes -#> 2024-07-19 16:13:20.254785 normalize expression +#> 2024-07-19 19:19:06.16668 make pseudobulk object +#> 2024-07-19 19:19:06.350406 drop lowly expressed genes +#> 2024-07-19 19:19:06.408463 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") -#> 2024-07-19 16:13:20.329602 create model matrix +#> 2024-07-19 19:19:06.490447 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) -#> 2024-07-19 16:13:20.34104 run duplicateCorrelation() -#> 2024-07-19 16:13:21.633985 The estimated correlation is: -0.0187869166526901 +#> 2024-07-19 19:19:06.502035 run duplicateCorrelation() +#> 2024-07-19 19:19:07.764039 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" ) -#> 2024-07-19 16:13:21.646473 computing F-statistics +#> 2024-07-19 19:19:07.776903 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" ) -#> 2024-07-19 16:13:21.70863 computing F-statistics +#> 2024-07-19 19:19:07.840921 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" ) -#> 2024-07-19 16:13:21.759248 computing F-statistics +#> 2024-07-19 19:19:07.893497 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 ddb4f8bb..c336588f 100644 --- a/reference/registration_stats_enrichment.html +++ b/reference/registration_stats_enrichment.html @@ -19,7 +19,7 @@ spatialLIBD - 1.17.6 + 1.17.7 @@ -171,9 +171,9 @@

Examples

#> #> rgstr_> ## Pseudo-bulk #> rgstr_> sce_pseudo <- registration_pseudobulk(sce, "Cell_Cycle", "sample_id", c("age"), min_ncells = NULL) -#> 2024-07-19 16:13:22.339711 make pseudobulk object -#> 2024-07-19 16:13:22.504956 drop lowly expressed genes -#> 2024-07-19 16:13:22.560832 normalize expression +#> 2024-07-19 19:19:08.486467 make pseudobulk object +#> 2024-07-19 19:19:08.639766 drop lowly expressed genes +#> 2024-07-19 19:19:08.695258 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") -#> 2024-07-19 16:13:22.635844 create model matrix +#> 2024-07-19 19:19:08.772091 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) -#> 2024-07-19 16:13:22.647296 run duplicateCorrelation() -#> 2024-07-19 16:13:23.968838 The estimated correlation is: -0.0187869166526901 +#> 2024-07-19 19:19:08.783674 run duplicateCorrelation() +#> 2024-07-19 19:19:10.072472 The estimated correlation is: -0.0187869166526901 results_enrichment <- registration_stats_enrichment(sce_pseudo, block_cor, "age", gene_ensembl = "ensembl", gene_name = "gene_name" ) -#> 2024-07-19 16:13:23.972511 computing enrichment statistics -#> 2024-07-19 16:13:24.092058 extract and reformat enrichment results +#> 2024-07-19 19:19:10.076253 computing enrichment statistics +#> 2024-07-19 19:19:10.196895 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" ) -#> 2024-07-19 16:13:24.125384 computing enrichment statistics -#> 2024-07-19 16:13:24.230207 extract and reformat enrichment results +#> 2024-07-19 19:19:10.230956 computing enrichment statistics +#> 2024-07-19 19:19:10.334255 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 f109605f..ab457798 100644 --- a/reference/registration_stats_pairwise.html +++ b/reference/registration_stats_pairwise.html @@ -20,7 +20,7 @@ spatialLIBD - 1.17.6 + 1.17.7 @@ -173,9 +173,9 @@

Examples

#> #> rgstr_> ## Pseudo-bulk #> rgstr_> sce_pseudo <- registration_pseudobulk(sce, "Cell_Cycle", "sample_id", c("age"), min_ncells = NULL) -#> 2024-07-19 16:13:24.698023 make pseudobulk object -#> 2024-07-19 16:13:24.856787 drop lowly expressed genes -#> 2024-07-19 16:13:24.912216 normalize expression +#> 2024-07-19 19:19:10.799806 make pseudobulk object +#> 2024-07-19 19:19:10.957315 drop lowly expressed genes +#> 2024-07-19 19:19:11.012869 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") -#> 2024-07-19 16:13:25.01452 create model matrix +#> 2024-07-19 19:19:11.115714 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) -#> 2024-07-19 16:13:25.02581 run duplicateCorrelation() -#> 2024-07-19 16:13:26.315256 The estimated correlation is: -0.0187869166526901 +#> 2024-07-19 19:19:11.12718 run duplicateCorrelation() +#> 2024-07-19 19:19:12.389345 The estimated correlation is: -0.0187869166526901 results_pairwise <- registration_stats_pairwise(sce_pseudo, registration_mod, block_cor, gene_ensembl = "ensembl", gene_name = "gene_name" ) -#> 2024-07-19 16:13:26.317262 running the baseline pairwise model -#> 2024-07-19 16:13:26.334045 computing pairwise statistics +#> 2024-07-19 19:19:12.391356 running the baseline pairwise model +#> 2024-07-19 19:19:12.40837 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" ) -#> 2024-07-19 16:13:26.399353 running the baseline pairwise model -#> 2024-07-19 16:13:26.416823 computing pairwise statistics +#> 2024-07-19 19:19:12.474836 running the baseline pairwise model +#> 2024-07-19 19:19:12.492762 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 3ee86b83..8fbe68a8 100644 --- a/reference/registration_wrapper.html +++ b/reference/registration_wrapper.html @@ -22,7 +22,7 @@ spatialLIBD - 1.17.6 + 1.17.7 @@ -200,18 +200,18 @@

Examples

sce, "Cell_Cycle", "sample_id", c("age"), "ensembl", "gene_name", "wrapper" ) -#> 2024-07-19 16:13:26.993961 make pseudobulk object -#> 2024-07-19 16:13:27.150164 dropping 9 pseudo-bulked samples that are below 'min_ncells'. -#> 2024-07-19 16:13:27.171914 drop lowly expressed genes -#> 2024-07-19 16:13:27.227205 normalize expression -#> 2024-07-19 16:13:27.28632 create model matrix -#> 2024-07-19 16:13:27.296998 run duplicateCorrelation() -#> 2024-07-19 16:13:29.726624 The estimated correlation is: -0.0783081238514532 -#> 2024-07-19 16:13:29.728866 computing enrichment statistics -#> 2024-07-19 16:13:29.849912 extract and reformat enrichment results -#> 2024-07-19 16:13:29.877506 running the baseline pairwise model -#> 2024-07-19 16:13:29.896565 computing pairwise statistics -#> 2024-07-19 16:13:29.973082 computing F-statistics +#> 2024-07-19 19:19:13.070737 make pseudobulk object +#> 2024-07-19 19:19:13.232868 dropping 9 pseudo-bulked samples that are below 'min_ncells'. +#> 2024-07-19 19:19:13.25428 drop lowly expressed genes +#> 2024-07-19 19:19:13.308777 normalize expression +#> 2024-07-19 19:19:13.366104 create model matrix +#> 2024-07-19 19:19:13.376468 run duplicateCorrelation() +#> 2024-07-19 19:19:15.772742 The estimated correlation is: -0.0783081238514532 +#> 2024-07-19 19:19:15.775038 computing enrichment statistics +#> 2024-07-19 19:19:15.898424 extract and reformat enrichment results +#> 2024-07-19 19:19:15.924931 running the baseline pairwise model +#> 2024-07-19 19:19:15.943354 computing pairwise statistics +#> 2024-07-19 19:19:16.018343 computing F-statistics diff --git a/reference/run_app.html b/reference/run_app.html index 2cca4ddc..2c161cba 100644 --- a/reference/run_app.html +++ b/reference/run_app.html @@ -19,7 +19,7 @@ spatialLIBD - 1.17.6 + 1.17.7 diff --git a/reference/sce_to_spe.html b/reference/sce_to_spe.html index 7cfda968..b637176c 100644 --- a/reference/sce_to_spe.html +++ b/reference/sce_to_spe.html @@ -21,7 +21,7 @@ spatialLIBD - 1.17.6 + 1.17.7 @@ -127,7 +127,7 @@

Examples

## Transform it to a SpatialExperiment object spe <- sce_to_spe(sce) } -#> 2024-07-19 16:13:32.995427 loading file /github/home/.cache/R/BiocFileCache/d681608cce0_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-07-19 19:19:18.228 loading file /github/home/.cache/R/BiocFileCache/db1206d4b6_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 c0accf5c..c7d04b3a 100644 --- a/reference/sig_genes_extract.html +++ b/reference/sig_genes_extract.html @@ -21,7 +21,7 @@ spatialLIBD - 1.17.6 + 1.17.7 @@ -156,9 +156,9 @@

Examples

if (!exists("modeling_results")) { modeling_results <- fetch_data(type = "modeling_results") } -#> 2024-07-19 16:13:46.662992 loading file /github/home/.cache/R/BiocFileCache/29a61439eba_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1 +#> 2024-07-19 19:19:31.185692 loading file /github/home/.cache/R/BiocFileCache/2e21996cc5_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1 if (!exists("sce_layer")) sce_layer <- fetch_data(type = "sce_layer") -#> 2024-07-19 16:13:47.945186 loading file /github/home/.cache/R/BiocFileCache/29a7aca31b5_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-07-19 19:19:32.224471 loading file /github/home/.cache/R/BiocFileCache/2e2552c8efc_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 c4118843..660ec8ab 100644 --- a/reference/sig_genes_extract_all.html +++ b/reference/sig_genes_extract_all.html @@ -19,7 +19,7 @@ spatialLIBD - 1.17.6 + 1.17.7 @@ -128,9 +128,9 @@

Examples

if (!exists("modeling_results")) { modeling_results <- fetch_data(type = "modeling_results") } -#> 2024-07-19 16:13:52.004175 loading file /github/home/.cache/R/BiocFileCache/29a61439eba_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1 +#> 2024-07-19 19:19:36.021553 loading file /github/home/.cache/R/BiocFileCache/2e21996cc5_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1 if (!exists("sce_layer")) sce_layer <- fetch_data(type = "sce_layer") -#> 2024-07-19 16:13:53.36229 loading file /github/home/.cache/R/BiocFileCache/29a7aca31b5_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-07-19 19:19:37.056471 loading file /github/home/.cache/R/BiocFileCache/2e2552c8efc_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 675c4397..2e16bce9 100644 --- a/reference/sort_clusters.html +++ b/reference/sort_clusters.html @@ -19,7 +19,7 @@ spatialLIBD - 1.17.6 + 1.17.7 diff --git a/reference/spatialLIBD-package.html b/reference/spatialLIBD-package.html index c22a18c2..1be434ca 100644 --- a/reference/spatialLIBD-package.html +++ b/reference/spatialLIBD-package.html @@ -18,7 +18,7 @@ spatialLIBD - 1.17.6 + 1.17.7 diff --git a/reference/tstats_Human_DLPFC_snRNAseq_Nguyen_topLayer.html b/reference/tstats_Human_DLPFC_snRNAseq_Nguyen_topLayer.html index 4dbbeb2a..2c95d0c7 100644 --- a/reference/tstats_Human_DLPFC_snRNAseq_Nguyen_topLayer.html +++ b/reference/tstats_Human_DLPFC_snRNAseq_Nguyen_topLayer.html @@ -23,7 +23,7 @@ spatialLIBD - 1.17.6 + 1.17.7 diff --git a/reference/vis_clus.html b/reference/vis_clus.html index 3c917c2e..76175248 100644 --- a/reference/vis_clus.html +++ b/reference/vis_clus.html @@ -19,7 +19,7 @@ spatialLIBD - 1.17.6 + 1.17.7 @@ -242,7 +242,7 @@

Examples

) print(p4) } -#> 2024-07-19 16:13:56.634793 loading file /github/home/.cache/R/BiocFileCache/d681608cce0_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-07-19 19:19:39.709647 loading file /github/home/.cache/R/BiocFileCache/db1206d4b6_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 9c46b335..e205079a 100644 --- a/reference/vis_clus_p.html +++ b/reference/vis_clus_p.html @@ -20,7 +20,7 @@ spatialLIBD - 1.17.6 + 1.17.7 @@ -202,7 +202,7 @@

Examples

## Clean up rm(spe_sub) } -#> 2024-07-19 16:14:17.058462 loading file /github/home/.cache/R/BiocFileCache/d681608cce0_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-07-19 19:19:58.875629 loading file /github/home/.cache/R/BiocFileCache/db1206d4b6_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 diff --git a/reference/vis_gene.html b/reference/vis_gene.html index fe6cb371..f64a8edc 100644 --- a/reference/vis_gene.html +++ b/reference/vis_gene.html @@ -20,7 +20,7 @@ spatialLIBD - 1.17.6 + 1.17.7 @@ -341,7 +341,7 @@

Examples

) print(p8) } -#> 2024-07-19 16:14:32.570921 loading file /github/home/.cache/R/BiocFileCache/d681608cce0_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-07-19 19:20:13.724161 loading file /github/home/.cache/R/BiocFileCache/db1206d4b6_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 cf7a1a90..a5c122f1 100644 --- a/reference/vis_gene_p.html +++ b/reference/vis_gene_p.html @@ -21,7 +21,7 @@ spatialLIBD - 1.17.6 + 1.17.7 @@ -215,7 +215,7 @@

Examples

## Clean up rm(spe_sub) } -#> 2024-07-19 16:14:59.279549 loading file /github/home/.cache/R/BiocFileCache/d681608cce0_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-07-19 19:20:39.958743 loading file /github/home/.cache/R/BiocFileCache/db1206d4b6_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 50b92b61..ac4329b3 100644 --- a/reference/vis_grid_clus.html +++ b/reference/vis_grid_clus.html @@ -19,7 +19,7 @@ spatialLIBD - 1.17.6 + 1.17.7 @@ -237,7 +237,7 @@

Examples

## for subject 3 cowplot::plot_grid(plotlist = p_list, ncol = 2) } -#> 2024-07-19 16:15:14.770951 loading file /github/home/.cache/R/BiocFileCache/d681608cce0_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-07-19 19:20:54.89049 loading file /github/home/.cache/R/BiocFileCache/db1206d4b6_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 73a87f80..eb4831c4 100644 --- a/reference/vis_grid_gene.html +++ b/reference/vis_grid_gene.html @@ -20,7 +20,7 @@ spatialLIBD - 1.17.6 + 1.17.7 @@ -256,7 +256,7 @@

Examples

## for subject 3 cowplot::plot_grid(plotlist = p_list, ncol = 2) } -#> 2024-07-19 16:15:31.676291 loading file /github/home/.cache/R/BiocFileCache/d681608cce0_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-07-19 19:21:11.275489 loading file /github/home/.cache/R/BiocFileCache/db1206d4b6_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1