From 71a3de43dcb71b1909478ff63ba136957859a530 Mon Sep 17 00:00:00 2001 From: Nick-Eagles <45461721+Nick-Eagles@users.noreply.github.com> Date: Thu, 31 Oct 2024 20:34:15 +0000 Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20LieberIn?= =?UTF-8?q?stitute/spatialLIBD@a87428b7675532ed6e38baba05be500b943389a8=20?= =?UTF-8?q?=F0=9F=9A=80?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- articles/TenX_data_download.html | 20 ++++++------- articles/guide_to_spatial_registration.html | 30 ++++++++++---------- articles/multi_gene_plots.html | 8 +++--- articles/spatialLIBD.html | 12 ++++---- pkgdown.yml | 2 +- reference/add_images.html | 26 ++++++++--------- reference/add_key.html | 2 +- reference/add_qc_metrics.html | 2 +- reference/annotate_registered_clusters.html | 2 +- reference/check_modeling_results.html | 2 +- reference/check_sce.html | 2 +- reference/check_sce_layer.html | 2 +- reference/check_spe.html | 2 +- reference/cluster_export.html | 2 +- reference/cluster_import.html | 6 ++-- reference/fetch_data.html | 2 +- reference/frame_limits.html | 2 +- reference/gene_set_enrichment.html | 2 +- reference/gene_set_enrichment_plot.html | 2 +- reference/geom_spatial.html | 2 +- reference/get_colors.html | 2 +- reference/img_edit.html | 2 +- reference/img_update.html | 2 +- reference/img_update_all.html | 2 +- reference/layer_boxplot.html | 4 +-- reference/layer_stat_cor.html | 2 +- reference/layer_stat_cor_plot.html | 2 +- reference/registration_block_cor.html | 12 ++++---- reference/registration_model.html | 8 +++--- reference/registration_pseudobulk.html | 6 ++-- reference/registration_stats_anova.html | 18 ++++++------ reference/registration_stats_enrichment.html | 20 ++++++------- reference/registration_stats_pairwise.html | 20 ++++++------- reference/registration_wrapper.html | 24 ++++++++-------- reference/sce_to_spe.html | 2 +- reference/sig_genes_extract.html | 4 +-- reference/sig_genes_extract_all.html | 4 +-- reference/vis_clus.html | 2 +- reference/vis_clus_p.html | 2 +- reference/vis_gene.html | 2 +- reference/vis_gene_p.html | 2 +- reference/vis_grid_clus.html | 2 +- reference/vis_grid_gene.html | 2 +- 43 files changed, 138 insertions(+), 138 deletions(-) diff --git a/articles/TenX_data_download.html b/articles/TenX_data_download.html index d9dcea0..d6f3309 100644 --- a/articles/TenX_data_download.html +++ b/articles/TenX_data_download.html @@ -531,8 +531,8 @@

From Gencode## Show the GTF cache location gtf_cache -#> BFC4 -#> "/github/home/.cache/R/BiocFileCache/f82afbc5ba_gencode.v32.annotation.gtf.gz" +#> BFC4 +#> "/github/home/.cache/R/BiocFileCache/4a1665ee0bf_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 ) -#> 2024-10-31 18:57:34.262805 SpatialExperiment::read10xVisium: reading basic data from SpaceRanger -#> 2024-10-31 18:57:46.035754 read10xVisiumAnalysis: reading analysis output from SpaceRanger -#> 2024-10-31 18:57:46.146036 add10xVisiumAnalysis: adding analysis output from SpaceRanger -#> 2024-10-31 18:57:46.402929 rtracklayer::import: reading the reference GTF file -#> 2024-10-31 18:58:14.551331 adding gene information to the SPE object +#> 2024-10-31 20:33:17.636373 SpatialExperiment::read10xVisium: reading basic data from SpaceRanger +#> 2024-10-31 20:33:29.208114 read10xVisiumAnalysis: reading analysis output from SpaceRanger +#> 2024-10-31 20:33:29.312782 add10xVisiumAnalysis: adding analysis output from SpaceRanger +#> 2024-10-31 20:33:29.55953 rtracklayer::import: reading the reference GTF file +#> 2024-10-31 20:33:57.419312 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. -#> 2024-10-31 18:58:14.816284 adding information used by spatialLIBD +#> 2024-10-31 20:33:57.674576 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] "2024-10-31 18:58:15 UTC"
+
#> [1] "2024-10-31 20:33:58 UTC"

Wallclock time spent generating the vignette.

-
#> Time difference of 1.706 mins
+
#> Time difference of 1.682 mins

R session information.

#> ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
 #>  setting  value
diff --git a/articles/guide_to_spatial_registration.html b/articles/guide_to_spatial_registration.html
index 4adc05e..ad1cd9a 100644
--- a/articles/guide_to_spatial_registration.html
+++ b/articles/guide_to_spatial_registration.html
@@ -288,7 +288,7 @@ 
Spatial Reference
 ## get reference layer enrichment statistics
 layer_modeling_results <- fetch_data(type = "modeling_results")
-#> 2024-10-31 18:54:40.700817 loading file /github/home/.cache/R/BiocFileCache/f8264bf867d_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
+#> 2024-10-31 20:30:20.090674 loading file /github/home/.cache/R/BiocFileCache/4a1260aa093_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"
 )
-#> 2024-10-31 18:54:48.448164 make pseudobulk object
-#> 2024-10-31 18:54:50.132408 dropping 13 pseudo-bulked samples that are below 'min_ncells'.
-#> 2024-10-31 18:54:50.197142 drop lowly expressed genes
-#> 2024-10-31 18:54:50.38858 normalize expression
-#> 2024-10-31 18:54:51.841425 create model matrix
-#> 2024-10-31 18:54:51.865055 run duplicateCorrelation()
-#> 2024-10-31 18:55:04.864228 The estimated correlation is: 0.138734774807097
-#> 2024-10-31 18:55:04.867043 computing enrichment statistics
-#> 2024-10-31 18:55:06.00789 extract and reformat enrichment results
-#> 2024-10-31 18:55:06.063235 running the baseline pairwise model
-#> 2024-10-31 18:55:06.20487 computing pairwise statistics
-#> 2024-10-31 18:55:07.56266 computing F-statistics

+#> 2024-10-31 20:30:27.935639 make pseudobulk object
+#> 2024-10-31 20:30:29.626031 dropping 13 pseudo-bulked samples that are below 'min_ncells'.
+#> 2024-10-31 20:30:29.686539 drop lowly expressed genes
+#> 2024-10-31 20:30:29.850742 normalize expression
+#> 2024-10-31 20:30:31.367735 create model matrix
+#> 2024-10-31 20:30:31.397973 run duplicateCorrelation()
+#> 2024-10-31 20:30:44.62648 The estimated correlation is: 0.138734774807097
+#> 2024-10-31 20:30:44.629237 computing enrichment statistics
+#> 2024-10-31 20:30:45.832523 extract and reformat enrichment results
+#> 2024-10-31 20:30:45.887797 running the baseline pairwise model
+#> 2024-10-31 20:30:46.027914 computing pairwise statistics
+#> 2024-10-31 20:30:47.409161 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] "2024-10-31 18:55:09 UTC"
+
#> [1] "2024-10-31 20:30:48 UTC"

Wallclock time spent generating the vignette.

-
#> Time difference of 40.364 secs
+
#> Time difference of 41.483 secs

R session information.

#> ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
 #>  setting  value
diff --git a/articles/multi_gene_plots.html b/articles/multi_gene_plots.html
index 9fc93f7..5a54b5f 100644
--- a/articles/multi_gene_plots.html
+++ b/articles/multi_gene_plots.html
@@ -195,9 +195,9 @@ 
Plotting One Gene
 modeling_results <- fetch_data(type = "modeling_results")
-#> 2024-10-31 18:55:33.768312 loading file /github/home/.cache/R/BiocFileCache/f8264bf867d_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
+#> 2024-10-31 20:31:14.755233 loading file /github/home/.cache/R/BiocFileCache/4a1260aa093_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
 sce_layer <- fetch_data(type = "sce_layer")
-#> 2024-10-31 18:55:34.6724 loading file /github/home/.cache/R/BiocFileCache/f82f362f0_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-10-31 20:31:15.950342 loading file /github/home/.cache/R/BiocFileCache/4a11f72b28f_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] "2024-10-31 18:55:50 UTC"

+
#> [1] "2024-10-31 20:31:32 UTC"

 
Wallclock time spent generating the vignette.

-
#> Time difference of 36.832 secs

+
#> Time difference of 37.985 secs

 
R session information.

 
#> ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
 #>  setting  value
diff --git a/articles/spatialLIBD.html b/articles/spatialLIBD.html
index 456f47a..dbb8f73 100644
--- a/articles/spatialLIBD.html
+++ b/articles/spatialLIBD.html
@@ -414,7 +414,7 @@ 
Downloading the data with s
 
 ## Download the small example sce data
 sce <- fetch_data(type = "sce_example", eh = ehub)
-#> 2024-10-31 18:56:06.554724 loading file /github/home/.cache/R/BiocFileCache/f825297dc9_sce_sub_for_vignette.Rdata%3Fdl%3D1
+#> 2024-10-31 20:31:48.544302 loading file /github/home/.cache/R/BiocFileCache/4a115950912_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)
-#> 2024-10-31 18:56:11.157008 loading file /github/home/.cache/R/BiocFileCache/f82f362f0_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-10-31 20:31:55.311001 loading file /github/home/.cache/R/BiocFileCache/4a11f72b28f_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
 modeling_results <- fetch_data("modeling_results", eh = ehub)
-#> 2024-10-31 18:56:11.635906 loading file /github/home/.cache/R/BiocFileCache/f8264bf867d_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1

+#> 2024-10-31 20:31:55.78616 loading file /github/home/.cache/R/BiocFileCache/4a1260aa093_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 
-#>   9.095   0.364   9.514
+#>   9.250   0.380   9.653
 
 ## Explore the result
 class(sig_genes)
@@ -1377,9 +1377,9 @@ 
Reproducibilitylibrary("knitr")
 knit("spatialLIBD.Rmd", tangle = TRUE)

 
Date the vignette was generated.

-
#> [1] "2024-10-31 18:56:29 UTC"

+
#> [1] "2024-10-31 20:32:13 UTC"

 
Wallclock time spent generating the vignette.

-
#> Time difference of 35.048 secs

+
#> Time difference of 37.911 secs

 
R session information.

 
#> ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
 #>  setting  value
diff --git a/pkgdown.yml b/pkgdown.yml
index 6a499a6..5d93643 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: 2024-10-31T18:48Z
+last_built: 2024-10-31T20:24Z
diff --git a/reference/add_images.html b/reference/add_images.html
index 6a16e54..d759c6c 100644
--- a/reference/add_images.html
+++ b/reference/add_images.html
@@ -165,29 +165,29 @@ 
Examples

         image_paths = c("151507" = "https://spatial-dlpfc.s3.us-east-2.amazonaws.com/images/151507_tissue_lowres_image.png")
     ))
 }
-#> 2024-10-31 18:48:58.496006 loading file /github/home/.cache/R/BiocFileCache/1a505c0e9a2d_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
-#> 2024-10-31 18:49:14.043829 adding image for sample 151507
-#> 2024-10-31 18:49:14.865949 adding image for sample 151508
+#> 2024-10-31 20:24:19.062387 loading file /github/home/.cache/R/BiocFileCache/f6f1918e278_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-10-31 20:24:34.560494 adding image for sample 151507
+#> 2024-10-31 20:24:36.193818 adding image for sample 151508
 #> Warning: No image was found for sample: 151508
-#> 2024-10-31 18:49:14.866718 adding image for sample 151509
+#> 2024-10-31 20:24:36.194563 adding image for sample 151509
 #> Warning: No image was found for sample: 151509
-#> 2024-10-31 18:49:14.86723 adding image for sample 151510
+#> 2024-10-31 20:24:36.195075 adding image for sample 151510
 #> Warning: No image was found for sample: 151510
-#> 2024-10-31 18:49:14.867716 adding image for sample 151669
+#> 2024-10-31 20:24:36.195568 adding image for sample 151669
 #> Warning: No image was found for sample: 151669
-#> 2024-10-31 18:49:14.868195 adding image for sample 151670
+#> 2024-10-31 20:24:36.196038 adding image for sample 151670
 #> Warning: No image was found for sample: 151670
-#> 2024-10-31 18:49:14.868701 adding image for sample 151671
+#> 2024-10-31 20:24:36.196534 adding image for sample 151671
 #> Warning: No image was found for sample: 151671
-#> 2024-10-31 18:49:14.869175 adding image for sample 151672
+#> 2024-10-31 20:24:36.197004 adding image for sample 151672
 #> Warning: No image was found for sample: 151672
-#> 2024-10-31 18:49:14.869679 adding image for sample 151673
+#> 2024-10-31 20:24:36.197478 adding image for sample 151673
 #> Warning: No image was found for sample: 151673
-#> 2024-10-31 18:49:14.870145 adding image for sample 151674
+#> 2024-10-31 20:24:36.19794 adding image for sample 151674
 #> Warning: No image was found for sample: 151674
-#> 2024-10-31 18:49:14.870613 adding image for sample 151675
+#> 2024-10-31 20:24:36.198402 adding image for sample 151675
 #> Warning: No image was found for sample: 151675
-#> 2024-10-31 18:49:14.871076 adding image for sample 151676
+#> 2024-10-31 20:24:36.198871 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 552bab8..f431e89 100644
--- a/reference/add_key.html
+++ b/reference/add_key.html
@@ -124,7 +124,7 @@ 
Examples

     spe$key_original <- NULL
     head(spe$key)
 }
-#> 2024-10-31 18:49:17.26523 loading file /github/home/.cache/R/BiocFileCache/1a505c0e9a2d_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-10-31 20:24:38.980763 loading file /github/home/.cache/R/BiocFileCache/f6f1918e278_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 119b36c..c16abd2 100644
--- a/reference/add_qc_metrics.html
+++ b/reference/add_qc_metrics.html
@@ -144,7 +144,7 @@ 
Author

     
Examples

     
## Obtain the necessary data
 spe_pre_qc <- fetch_data("spatialDLPFC_Visium_example_subset")
-#> 2024-10-31 18:49:32.822732 loading file /github/home/.cache/R/BiocFileCache/f82775a1a2_spatialDLPFC_spe_subset_example.rds%3Fdl%3D1
+#> 2024-10-31 20:24:55.026698 loading file /github/home/.cache/R/BiocFileCache/4a160c71130_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 ca8a83e..ee2b27d 100644
--- a/reference/annotate_registered_clusters.html
+++ b/reference/annotate_registered_clusters.html
@@ -137,7 +137,7 @@ 
Examples

 if (!exists("modeling_results")) {
     modeling_results <- fetch_data(type = "modeling_results")
 }
-#> 2024-10-31 18:49:44.893063 loading file /github/home/.cache/R/BiocFileCache/f8264bf867d_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
+#> 2024-10-31 20:25:07.681774 loading file /github/home/.cache/R/BiocFileCache/4a1260aa093_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 2ce0820..2f490be 100644
--- a/reference/check_modeling_results.html
+++ b/reference/check_modeling_results.html
@@ -108,7 +108,7 @@ 
Examples

 if (!exists("modeling_results")) {
     modeling_results <- fetch_data(type = "modeling_results")
 }
-#> 2024-10-31 18:49:45.937878 loading file /github/home/.cache/R/BiocFileCache/f8264bf867d_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
+#> 2024-10-31 20:25:09.047655 loading file /github/home/.cache/R/BiocFileCache/4a1260aa093_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 020591c..0178a36 100644
--- a/reference/check_sce.html
+++ b/reference/check_sce.html
@@ -131,7 +131,7 @@ 
Examples

     ## Check the object
     check_sce(sce_example)
 }
-#> 2024-10-31 18:49:47.029589 loading file /github/home/.cache/R/BiocFileCache/f825297dc9_sce_sub_for_vignette.Rdata%3Fdl%3D1
+#> 2024-10-31 20:25:10.442552 loading file /github/home/.cache/R/BiocFileCache/4a115950912_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 3488d46..84c1ec5 100644
--- a/reference/check_sce_layer.html
+++ b/reference/check_sce_layer.html
@@ -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")
-#> 2024-10-31 18:49:49.494754 loading file /github/home/.cache/R/BiocFileCache/f82f362f0_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-10-31 20:25:13.134764 loading file /github/home/.cache/R/BiocFileCache/4a11f72b28f_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 1c16394..e345ef2 100644
--- a/reference/check_spe.html
+++ b/reference/check_spe.html
@@ -123,7 +123,7 @@ 
Examples

     ## Check the object
     check_spe(spe)
 }
-#> 2024-10-31 18:49:50.682719 loading file /github/home/.cache/R/BiocFileCache/1a505c0e9a2d_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-10-31 20:25:14.606332 loading file /github/home/.cache/R/BiocFileCache/f6f1918e278_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 ecda17a..a0cf464 100644
--- a/reference/cluster_export.html
+++ b/reference/cluster_export.html
@@ -134,7 +134,7 @@ 
Examples

     cluster_export(spe, "spatialLIBD")
     cluster_export(spe, "GraphBased")
 }
-#> 2024-10-31 18:50:05.203212 loading file /github/home/.cache/R/BiocFileCache/1a505c0e9a2d_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-10-31 20:25:30.508778 loading file /github/home/.cache/R/BiocFileCache/f6f1918e278_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 cede311..3e213df 100644
--- a/reference/cluster_import.html
+++ b/reference/cluster_import.html
@@ -137,11 +137,11 @@ 
Examples

     ## Re-import them
     colData(cluster_import(spe))
 }
-#> 2024-10-31 18:50:20.298152 loading file /github/home/.cache/R/BiocFileCache/1a505c0e9a2d_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-10-31 20:25:45.336307 loading file /github/home/.cache/R/BiocFileCache/f6f1918e278_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
 #> Overwriting 'spe$key'. Set 'overwrite = FALSE' if you do not want to overwrite it.
-#> Warning: '/tmp/Rtmp4F4wAy/exported_clusters/spatialLIBD' already exists
+#> Warning: '/tmp/RtmpgTDK7X/exported_clusters/spatialLIBD' already exists
 #> Overwriting 'spe$key'. Set 'overwrite = FALSE' if you do not want to overwrite it.
-#> Warning: '/tmp/Rtmp4F4wAy/exported_clusters/GraphBased' already exists
+#> Warning: '/tmp/RtmpgTDK7X/exported_clusters/GraphBased' already exists
 #> Overwriting 'spe$key'. Set 'overwrite = FALSE' if you do not want to overwrite it.
 #> DataFrame with 47681 rows and 71 columns
 #>                                       key   sample_id   Cluster   sum_umi
diff --git a/reference/fetch_data.html b/reference/fetch_data.html
index 3a00c57..e50775c 100644
--- a/reference/fetch_data.html
+++ b/reference/fetch_data.html
@@ -166,7 +166,7 @@ 
Examples

 ## Download the SingleCellExperiment object
 ## at the layer-level
 if (!exists("sce_layer")) sce_layer <- fetch_data("sce_layer")
-#> 2024-10-31 18:50:35.589725 loading file /github/home/.cache/R/BiocFileCache/f82f362f0_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-10-31 20:26:02.186012 loading file /github/home/.cache/R/BiocFileCache/4a11f72b28f_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 919162e..8a81be9 100644
--- a/reference/frame_limits.html
+++ b/reference/frame_limits.html
@@ -154,7 +154,7 @@ 
Examples

     ## Obtain the frame limits for one sample
     frame_limits(spe, sampleid = "151673")
 }
-#> 2024-10-31 18:50:37.261539 loading file /github/home/.cache/R/BiocFileCache/1a505c0e9a2d_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-10-31 20:26:04.315375 loading file /github/home/.cache/R/BiocFileCache/f6f1918e278_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 7433abd..f68c5ef 100644
--- a/reference/gene_set_enrichment.html
+++ b/reference/gene_set_enrichment.html
@@ -176,7 +176,7 @@ 
Examples

 if (!exists("modeling_results")) {
     modeling_results <- fetch_data(type = "modeling_results")
 }
-#> 2024-10-31 18:50:52.253886 loading file /github/home/.cache/R/BiocFileCache/f8264bf867d_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
+#> 2024-10-31 20:26:20.646987 loading file /github/home/.cache/R/BiocFileCache/4a1260aa093_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 5bccd9e..36479f4 100644
--- a/reference/gene_set_enrichment_plot.html
+++ b/reference/gene_set_enrichment_plot.html
@@ -178,7 +178,7 @@ 
Examples

 if (!exists("modeling_results")) {
     modeling_results <- fetch_data(type = "modeling_results")
 }
-#> 2024-10-31 18:50:53.482071 loading file /github/home/.cache/R/BiocFileCache/f8264bf867d_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
+#> 2024-10-31 20:26:22.286728 loading file /github/home/.cache/R/BiocFileCache/4a1260aa093_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 9f9360f..aeaa0d8 100644
--- a/reference/geom_spatial.html
+++ b/reference/geom_spatial.html
@@ -175,7 +175,7 @@ 
Examples

     ## Clean up
     rm(spe_sub)
 }
-#> 2024-10-31 18:50:55.186153 loading file /github/home/.cache/R/BiocFileCache/1a505c0e9a2d_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-10-31 20:26:24.415304 loading file /github/home/.cache/R/BiocFileCache/f6f1918e278_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
 
 

     
diff --git a/reference/get_colors.html b/reference/get_colors.html
index 6bba79c..6eb9c01 100644
--- a/reference/get_colors.html
+++ b/reference/get_colors.html
@@ -105,7 +105,7 @@ 
Examples

     

 ## Obtain the necessary data
 if (!exists("sce_layer")) sce_layer <- fetch_data("sce_layer")
-#> 2024-10-31 18:51:10.427585 loading file /github/home/.cache/R/BiocFileCache/f82f362f0_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-10-31 20:26:40.291074 loading file /github/home/.cache/R/BiocFileCache/4a11f72b28f_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 edbba06..339041a 100644
--- a/reference/img_edit.html
+++ b/reference/img_edit.html
@@ -222,7 +222,7 @@ 
Examples

     x <- img_edit(spe, sampleid = "151507", brightness = 25)
     plot(x)
 }
-#> 2024-10-31 18:51:11.53543 loading file /github/home/.cache/R/BiocFileCache/1a505c0e9a2d_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-10-31 20:26:41.819093 loading file /github/home/.cache/R/BiocFileCache/f6f1918e278_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
 
 

     
diff --git a/reference/img_update.html b/reference/img_update.html
index 11c3859..093c497 100644
--- a/reference/img_update.html
+++ b/reference/img_update.html
@@ -139,7 +139,7 @@ 
Examples

     ## Reduce brightness to 25% and update the imgData()
     imgData(img_update(spe, sampleid = "151507", brightness = 25))
 }
-#> 2024-10-31 18:51:27.273337 loading file /github/home/.cache/R/BiocFileCache/1a505c0e9a2d_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-10-31 20:26:57.861005 loading file /github/home/.cache/R/BiocFileCache/f6f1918e278_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 37ea94d..1c2a781 100644
--- a/reference/img_update_all.html
+++ b/reference/img_update_all.html
@@ -138,7 +138,7 @@ 
Examples

     ## update the imgData()
     imgData(img_update_all(spe, brightness = 25))
 }
-#> 2024-10-31 18:51:41.599181 loading file /github/home/.cache/R/BiocFileCache/1a505c0e9a2d_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-10-31 20:27:12.503589 loading file /github/home/.cache/R/BiocFileCache/f6f1918e278_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
 #> DataFrame with 24 rows and 4 columns
 #>       sample_id      image_id   data scaleFactor
 #>     <character>   <character> <list>   <numeric>
diff --git a/reference/layer_boxplot.html b/reference/layer_boxplot.html
index 23c9fcf..2469628 100644
--- a/reference/layer_boxplot.html
+++ b/reference/layer_boxplot.html
@@ -185,9 +185,9 @@ 
Examples

 if (!exists("modeling_results")) {
     modeling_results <- fetch_data(type = "modeling_results")
 }
-#> 2024-10-31 18:51:58.482933 loading file /github/home/.cache/R/BiocFileCache/f8264bf867d_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
+#> 2024-10-31 20:27:29.766162 loading file /github/home/.cache/R/BiocFileCache/4a1260aa093_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
 if (!exists("sce_layer")) sce_layer <- fetch_data(type = "sce_layer")
-#> 2024-10-31 18:51:59.289894 loading file /github/home/.cache/R/BiocFileCache/f82f362f0_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-10-31 20:27:30.976263 loading file /github/home/.cache/R/BiocFileCache/4a11f72b28f_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
 
 ## Top 2 genes from the enrichment model
 sig_genes <- sig_genes_extract_all(
diff --git a/reference/layer_stat_cor.html b/reference/layer_stat_cor.html
index 1731d2a..ef6d46b 100644
--- a/reference/layer_stat_cor.html
+++ b/reference/layer_stat_cor.html
@@ -156,7 +156,7 @@ 
Examples

 if (!exists("modeling_results")) {
     modeling_results <- fetch_data(type = "modeling_results")
 }
-#> 2024-10-31 18:52:02.686341 loading file /github/home/.cache/R/BiocFileCache/f8264bf867d_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
+#> 2024-10-31 20:27:34.95313 loading file /github/home/.cache/R/BiocFileCache/4a1260aa093_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 fb65954..d9b87d7 100644
--- a/reference/layer_stat_cor_plot.html
+++ b/reference/layer_stat_cor_plot.html
@@ -145,7 +145,7 @@ 
Examples

 if (!exists("modeling_results")) {
     modeling_results <- fetch_data(type = "modeling_results")
 }
-#> 2024-10-31 18:52:03.84078 loading file /github/home/.cache/R/BiocFileCache/f8264bf867d_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
+#> 2024-10-31 20:27:36.412057 loading file /github/home/.cache/R/BiocFileCache/4a1260aa093_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
 
 ## Compute the correlations
 cor_stats_layer <- layer_stat_cor(
diff --git a/reference/registration_block_cor.html b/reference/registration_block_cor.html
index a5771ef..0741bbd 100644
--- a/reference/registration_block_cor.html
+++ b/reference/registration_block_cor.html
@@ -146,9 +146,9 @@ 
Examples

 #> 
 #> rgstr_> ## Pseudo-bulk
 #> rgstr_> sce_pseudo <- registration_pseudobulk(sce, "Cell_Cycle", "sample_id", c("age"), min_ncells = NULL)
-#> 2024-10-31 18:52:06.936542 make pseudobulk object
-#> 2024-10-31 18:52:07.146255 drop lowly expressed genes
-#> 2024-10-31 18:52:07.21465 normalize expression
+#> 2024-10-31 20:27:39.588807 make pseudobulk object
+#> 2024-10-31 20:27:39.816979 drop lowly expressed genes
+#> 2024-10-31 20:27:39.899263 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")
-#> 2024-10-31 18:52:07.293028 create model matrix
+#> 2024-10-31 20:27:39.982418 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)
-#> 2024-10-31 18:52:07.305342 run duplicateCorrelation()
-#> 2024-10-31 18:52:08.538288 The estimated correlation is: -0.0187869166526901
+#> 2024-10-31 20:27:39.995663 run duplicateCorrelation()
+#> 2024-10-31 20:27:41.290589 The estimated correlation is: -0.0187869166526901
diff --git a/reference/registration_model.html b/reference/registration_model.html index 7f93f19..0afd0d8 100644 --- a/reference/registration_model.html +++ b/reference/registration_model.html @@ -148,9 +148,9 @@

Examples

#> #> rgstr_> ## Pseudo-bulk #> rgstr_> sce_pseudo <- registration_pseudobulk(sce, "Cell_Cycle", "sample_id", c("age"), min_ncells = NULL) -#> 2024-10-31 18:52:08.969812 make pseudobulk object -#> 2024-10-31 18:52:09.158157 drop lowly expressed genes -#> 2024-10-31 18:52:09.212233 normalize expression +#> 2024-10-31 20:27:41.727388 make pseudobulk object +#> 2024-10-31 20:27:41.920928 drop lowly expressed genes +#> 2024-10-31 20:27:41.979309 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") -#> 2024-10-31 18:52:09.287272 create model matrix +#> 2024-10-31 20:27:42.054168 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 37a357d..360b773 100644 --- a/reference/registration_pseudobulk.html +++ b/reference/registration_pseudobulk.html @@ -159,9 +159,9 @@

Examples

## Pseudo-bulk sce_pseudo <- registration_pseudobulk(sce, "Cell_Cycle", "sample_id", c("age"), min_ncells = NULL) -#> 2024-10-31 18:52:09.705171 make pseudobulk object -#> 2024-10-31 18:52:09.887149 drop lowly expressed genes -#> 2024-10-31 18:52:09.941043 normalize expression +#> 2024-10-31 20:27:42.476538 make pseudobulk object +#> 2024-10-31 20:27:42.662947 drop lowly expressed genes +#> 2024-10-31 20:27:42.717835 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 64eff65..09ed71d 100644 --- a/reference/registration_stats_anova.html +++ b/reference/registration_stats_anova.html @@ -180,9 +180,9 @@

Examples

#> #> rgstr_> ## Pseudo-bulk #> rgstr_> sce_pseudo <- registration_pseudobulk(sce, "Cell_Cycle", "sample_id", c("age"), min_ncells = NULL) -#> 2024-10-31 18:52:10.531464 make pseudobulk object -#> 2024-10-31 18:52:10.691017 drop lowly expressed genes -#> 2024-10-31 18:52:10.745594 normalize expression +#> 2024-10-31 20:27:43.330647 make pseudobulk object +#> 2024-10-31 20:27:43.48633 drop lowly expressed genes +#> 2024-10-31 20:27:43.542063 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") -#> 2024-10-31 18:52:10.820926 create model matrix +#> 2024-10-31 20:27:43.618136 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) -#> 2024-10-31 18:52:10.832706 run duplicateCorrelation() -#> 2024-10-31 18:52:12.092901 The estimated correlation is: -0.0187869166526901 +#> 2024-10-31 20:27:43.63019 run duplicateCorrelation() +#> 2024-10-31 20:27:44.946026 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" ) -#> 2024-10-31 18:52:12.104628 computing F-statistics +#> 2024-10-31 20:27:44.95863 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" ) -#> 2024-10-31 18:52:12.165401 computing F-statistics +#> 2024-10-31 20:27:45.027015 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" ) -#> 2024-10-31 18:52:12.215062 computing F-statistics +#> 2024-10-31 20:27:45.077416 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 16d3d30..7412d21 100644 --- a/reference/registration_stats_enrichment.html +++ b/reference/registration_stats_enrichment.html @@ -171,9 +171,9 @@

Examples

#> #> rgstr_> ## Pseudo-bulk #> rgstr_> sce_pseudo <- registration_pseudobulk(sce, "Cell_Cycle", "sample_id", c("age"), min_ncells = NULL) -#> 2024-10-31 18:52:12.738353 make pseudobulk object -#> 2024-10-31 18:52:12.918049 drop lowly expressed genes -#> 2024-10-31 18:52:12.971146 normalize expression +#> 2024-10-31 20:27:45.608077 make pseudobulk object +#> 2024-10-31 20:27:45.794401 drop lowly expressed genes +#> 2024-10-31 20:27:45.850316 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") -#> 2024-10-31 18:52:13.04387 create model matrix +#> 2024-10-31 20:27:45.925474 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) -#> 2024-10-31 18:52:13.055277 run duplicateCorrelation() -#> 2024-10-31 18:52:14.290532 The estimated correlation is: -0.0187869166526901 +#> 2024-10-31 20:27:45.937309 run duplicateCorrelation() +#> 2024-10-31 20:27:47.229975 The estimated correlation is: -0.0187869166526901 results_enrichment <- registration_stats_enrichment(sce_pseudo, block_cor, "age", gene_ensembl = "ensembl", gene_name = "gene_name" ) -#> 2024-10-31 18:52:14.293854 computing enrichment statistics -#> 2024-10-31 18:52:14.411945 extract and reformat enrichment results +#> 2024-10-31 20:27:47.233631 computing enrichment statistics +#> 2024-10-31 20:27:47.352396 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" ) -#> 2024-10-31 18:52:14.44461 computing enrichment statistics -#> 2024-10-31 18:52:14.548669 extract and reformat enrichment results +#> 2024-10-31 20:27:47.385547 computing enrichment statistics +#> 2024-10-31 20:27:47.488791 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 fb78104..9fa962f 100644 --- a/reference/registration_stats_pairwise.html +++ b/reference/registration_stats_pairwise.html @@ -173,9 +173,9 @@

Examples

#> #> rgstr_> ## Pseudo-bulk #> rgstr_> sce_pseudo <- registration_pseudobulk(sce, "Cell_Cycle", "sample_id", c("age"), min_ncells = NULL) -#> 2024-10-31 18:52:15.023097 make pseudobulk object -#> 2024-10-31 18:52:15.179081 drop lowly expressed genes -#> 2024-10-31 18:52:15.232811 normalize expression +#> 2024-10-31 20:27:47.96792 make pseudobulk object +#> 2024-10-31 20:27:48.129766 drop lowly expressed genes +#> 2024-10-31 20:27:48.183394 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") -#> 2024-10-31 18:52:15.306272 create model matrix +#> 2024-10-31 20:27:48.256356 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) -#> 2024-10-31 18:52:15.317595 run duplicateCorrelation() -#> 2024-10-31 18:52:16.583224 The estimated correlation is: -0.0187869166526901 +#> 2024-10-31 20:27:48.267876 run duplicateCorrelation() +#> 2024-10-31 20:27:49.57912 The estimated correlation is: -0.0187869166526901 results_pairwise <- registration_stats_pairwise(sce_pseudo, registration_mod, block_cor, gene_ensembl = "ensembl", gene_name = "gene_name" ) -#> 2024-10-31 18:52:16.58498 running the baseline pairwise model -#> 2024-10-31 18:52:16.601265 computing pairwise statistics +#> 2024-10-31 20:27:49.58132 running the baseline pairwise model +#> 2024-10-31 20:27:49.598271 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" ) -#> 2024-10-31 18:52:16.665739 running the baseline pairwise model -#> 2024-10-31 18:52:16.683061 computing pairwise statistics +#> 2024-10-31 20:27:49.663743 running the baseline pairwise model +#> 2024-10-31 20:27:49.681207 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 8143af7..ab063d8 100644 --- a/reference/registration_wrapper.html +++ b/reference/registration_wrapper.html @@ -205,18 +205,18 @@

Examples

gene_name = "gene_name", suffix = "wrapper" ) -#> 2024-10-31 18:52:17.192737 make pseudobulk object -#> 2024-10-31 18:52:17.343534 dropping 9 pseudo-bulked samples that are below 'min_ncells'. -#> 2024-10-31 18:52:17.365098 drop lowly expressed genes -#> 2024-10-31 18:52:17.418148 normalize expression -#> 2024-10-31 18:52:17.475398 create model matrix -#> 2024-10-31 18:52:17.486057 run duplicateCorrelation() -#> 2024-10-31 18:52:19.868602 The estimated correlation is: -0.0783081238514532 -#> 2024-10-31 18:52:19.871077 computing enrichment statistics -#> 2024-10-31 18:52:19.984885 extract and reformat enrichment results -#> 2024-10-31 18:52:20.00999 running the baseline pairwise model -#> 2024-10-31 18:52:20.028215 computing pairwise statistics -#> 2024-10-31 18:52:20.101362 computing F-statistics +#> 2024-10-31 20:27:50.212626 make pseudobulk object +#> 2024-10-31 20:27:50.362406 dropping 9 pseudo-bulked samples that are below 'min_ncells'. +#> 2024-10-31 20:27:50.383501 drop lowly expressed genes +#> 2024-10-31 20:27:50.436933 normalize expression +#> 2024-10-31 20:27:50.494299 create model matrix +#> 2024-10-31 20:27:50.505118 run duplicateCorrelation() +#> 2024-10-31 20:27:52.985647 The estimated correlation is: -0.0783081238514532 +#> 2024-10-31 20:27:52.988182 computing enrichment statistics +#> 2024-10-31 20:27:53.104357 extract and reformat enrichment results +#> 2024-10-31 20:27:53.130206 running the baseline pairwise model +#> 2024-10-31 20:27:53.148322 computing pairwise statistics +#> 2024-10-31 20:27:53.223214 computing F-statistics ## Explore the results from registration_wrapper() class(example_modeling_results) diff --git a/reference/sce_to_spe.html b/reference/sce_to_spe.html index 6fb276e..f54cb73 100644 --- a/reference/sce_to_spe.html +++ b/reference/sce_to_spe.html @@ -127,7 +127,7 @@

Examples

## Transform it to a SpatialExperiment object spe <- sce_to_spe(sce) } -#> 2024-10-31 18:52:22.08008 loading file /github/home/.cache/R/BiocFileCache/1a505c0e9a2d_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-10-31 20:27:55.895246 loading file /github/home/.cache/R/BiocFileCache/f6f1918e278_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 5471299..bfa8b52 100644 --- a/reference/sig_genes_extract.html +++ b/reference/sig_genes_extract.html @@ -156,9 +156,9 @@

Examples

if (!exists("modeling_results")) { modeling_results <- fetch_data(type = "modeling_results") } -#> 2024-10-31 18:52:36.192924 loading file /github/home/.cache/R/BiocFileCache/f8264bf867d_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1 +#> 2024-10-31 20:28:09.439362 loading file /github/home/.cache/R/BiocFileCache/4a1260aa093_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1 if (!exists("sce_layer")) sce_layer <- fetch_data(type = "sce_layer") -#> 2024-10-31 18:52:37.000669 loading file /github/home/.cache/R/BiocFileCache/f82f362f0_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-10-31 20:28:10.657705 loading file /github/home/.cache/R/BiocFileCache/4a11f72b28f_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 993ea51..dffecb8 100644 --- a/reference/sig_genes_extract_all.html +++ b/reference/sig_genes_extract_all.html @@ -128,9 +128,9 @@

Examples

if (!exists("modeling_results")) { modeling_results <- fetch_data(type = "modeling_results") } -#> 2024-10-31 18:52:39.255903 loading file /github/home/.cache/R/BiocFileCache/f8264bf867d_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1 +#> 2024-10-31 20:28:14.031199 loading file /github/home/.cache/R/BiocFileCache/4a1260aa093_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1 if (!exists("sce_layer")) sce_layer <- fetch_data(type = "sce_layer") -#> 2024-10-31 18:52:40.152414 loading file /github/home/.cache/R/BiocFileCache/f82f362f0_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-10-31 20:28:15.238751 loading file /github/home/.cache/R/BiocFileCache/4a11f72b28f_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1 ## top 10 genes for all models sig_genes_extract_all( diff --git a/reference/vis_clus.html b/reference/vis_clus.html index 2263a35..efc1d7f 100644 --- a/reference/vis_clus.html +++ b/reference/vis_clus.html @@ -242,7 +242,7 @@

Examples

) print(p4) } -#> 2024-10-31 18:52:42.522765 loading file /github/home/.cache/R/BiocFileCache/1a505c0e9a2d_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-10-31 20:28:18.021968 loading file /github/home/.cache/R/BiocFileCache/f6f1918e278_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 73c1042..eab1883 100644 --- a/reference/vis_clus_p.html +++ b/reference/vis_clus_p.html @@ -202,7 +202,7 @@

Examples

## Clean up rm(spe_sub) } -#> 2024-10-31 18:53:01.476409 loading file /github/home/.cache/R/BiocFileCache/1a505c0e9a2d_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-10-31 20:28:37.921685 loading file /github/home/.cache/R/BiocFileCache/f6f1918e278_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 diff --git a/reference/vis_gene.html b/reference/vis_gene.html index d2ef4a7..e61a162 100644 --- a/reference/vis_gene.html +++ b/reference/vis_gene.html @@ -341,7 +341,7 @@

Examples

) print(p8) } -#> 2024-10-31 18:53:16.370041 loading file /github/home/.cache/R/BiocFileCache/1a505c0e9a2d_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-10-31 20:28:53.312282 loading file /github/home/.cache/R/BiocFileCache/f6f1918e278_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 c0f4fd7..e977a38 100644 --- a/reference/vis_gene_p.html +++ b/reference/vis_gene_p.html @@ -215,7 +215,7 @@

Examples

## Clean up rm(spe_sub) } -#> 2024-10-31 18:53:42.081996 loading file /github/home/.cache/R/BiocFileCache/1a505c0e9a2d_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-10-31 20:29:19.803842 loading file /github/home/.cache/R/BiocFileCache/f6f1918e278_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 6172017..4f9b6b9 100644 --- a/reference/vis_grid_clus.html +++ b/reference/vis_grid_clus.html @@ -237,7 +237,7 @@

Examples

## for subject 3 cowplot::plot_grid(plotlist = p_list, ncol = 2) } -#> 2024-10-31 18:53:57.047008 loading file /github/home/.cache/R/BiocFileCache/1a505c0e9a2d_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-10-31 20:29:35.17602 loading file /github/home/.cache/R/BiocFileCache/f6f1918e278_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 7e81c99..ce92d7d 100644 --- a/reference/vis_grid_gene.html +++ b/reference/vis_grid_gene.html @@ -256,7 +256,7 @@

Examples

## for subject 3 cowplot::plot_grid(plotlist = p_list, ncol = 2) } -#> 2024-10-31 18:54:13.333182 loading file /github/home/.cache/R/BiocFileCache/1a505c0e9a2d_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-10-31 20:29:51.87273 loading file /github/home/.cache/R/BiocFileCache/f6f1918e278_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1