Merge remote-tracking branch 'origin/main' into feature/denoising/upd…

…ate-results
openproblems-bio · Dec 19, 2024 · 4514312 · 4514312
2 parents 2ae73d9 + 7c9c0db
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diff --git a/.github/workflows/quarto_netlify.yml b/.github/workflows/quarto_netlify.yml
@@ -2,11 +2,6 @@ on:
   push:
     branches: [ main ]
   pull_request:
-    types:
-      - opened
-      - reopened
-      - synchronize
-      - closed
 
 name: Render project
 
@@ -57,7 +52,7 @@ jobs:
 
       - name: If PR, cache several directories
         if: github.event_name == 'pull_request'
-        uses: actions/cache@v2
+        uses: actions/cache@v4
         with:
           key: quarto-${{ github.ref_name }}
           restore-keys: quarto
@@ -128,4 +123,4 @@ jobs:
           message: |
             [![Deploy: failure](https://img.shields.io/badge/Deploy-failure-critical)](https://github.com/${{github.repository}}/actions/runs/${{github.run_id}}/jobs/${{github.job}})
           comment_tag: deploy_status
-
+
diff --git a/.gitignore b/.gitignore
@@ -8,8 +8,11 @@
 /.quarto/
 /_site
 /_freeze
+# local created libraries
+/results/*/library.bib
 
 # Temporary files generated by quarto preview
 /site_libs
 *.rmarkdown
 /.luarc.json
+/tmp
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -14,12 +14,20 @@
 
 * Update base images documentation (PR #342).
 
-* Add foundation models benchmark page (PR #354)
+* Add foundation models benchmark page (PR #354).
+
+* Add url to benchmark datasets to dataset page (PR #362).
+
+* Change "n x m" to "n cells × m genes" on dataset info (PR #362).
 
 ## BUG FIXES
 
 * Fix error in summary figure when not all method info ids are present in the results (PR #330).
 
+* Fix "used in" section in dataset pages (PR #362).
+
+* Rescale resources in funkyheatmap when methods and/or datasets are filtered (PR #368).
+
 # openproblems.bio v2.3.6
 
 ## NEW CONTENT

diff --git a/datasets/10x_datasets/human_colorectal_cancer_visium/index.qmd b/datasets/10x_datasets/human_colorectal_cancer_visium/index.qmd
diff --git a/datasets/_include/_index_template.qmd b/datasets/_include/_index_template.qmd
@@ -122,7 +122,7 @@ metadata <- tribble(
   "Reference", "bi bi-file-earmark-text", paste0("@", uns$dataset_reference),
   "Size", "bi bi-cloud-download", file_size_str,
   "Created", "bi bi-calendar", uns$date_created,
-  "Dimensions", "bi bi-box", shape_str
+  "Dimensions", "bi bi-box", glue::glue("{shape[[1]]} cells × {shape[[2]]} genes")
 )
 metadata_lines <- paste0(
   "<i class=\"", metadata$icon, "\"></i> ", substitute_underscores(metadata$value), "  \n"
@@ -169,7 +169,8 @@ cat("#### Used in\n\n")
 if (nrow(related_tasks) == 0) {
   cat("No related benchmarks found.\n")
 } else {
-  links <- paste0("* [", related_tasks$task_name, "](/results/", related_tasks$task_id, ")  ")
+  task_id <- gsub("task_", "", related_tasks$task_id)
+  links <- paste0("* [", related_tasks$task_name, "](/results/", task_id, ")  ")
   cat(paste(links, collapse = "\n"))
 }
 

diff --git a/..._cancer_xenium/data/dataset_metadata.json → ...n_colon_cancer/data/dataset_metadata.json b/..._cancer_xenium/data/dataset_metadata.json → ...n_colon_cancer/data/dataset_metadata.json
@@ -8,17 +8,17 @@
         "name": "counts",
         "schema_type": "integer",
         "shape": [
-          5514,
-          14015
+          5561,
+          14016
         ],
         "type": "sparsematrix"
       },
       {
         "dtype": "float32",
         "name": "normalized",
         "shape": [
-          5514,
-          14015
+          5561,
+          14016
         ],
         "type": "sparsematrix"
       }
@@ -28,103 +28,103 @@
         "dtype": "int64",
         "name": "in_tissue",
         "shape": [
-          5514
+          5561
         ],
         "type": "vector"
       },
       {
         "dtype": "int64",
         "name": "array_row",
         "shape": [
-          5514
+          5561
         ],
         "type": "vector"
       },
       {
         "dtype": "int64",
         "name": "array_col",
         "shape": [
-          5514
+          5561
         ],
         "type": "vector"
       },
       {
         "dtype": "int32",
         "name": "n_genes_by_counts",
         "shape": [
-          5514
+          5561
         ],
         "type": "vector"
       },
       {
         "dtype": "float64",
         "name": "log1p_n_genes_by_counts",
         "shape": [
-          5514
+          5561
         ],
         "type": "vector"
       },
       {
         "dtype": "float32",
         "name": "total_counts",
         "shape": [
-          5514
+          5561
         ],
         "type": "vector"
       },
       {
         "dtype": "float32",
         "name": "log1p_total_counts",
         "shape": [
-          5514
+          5561
         ],
         "type": "vector"
       },
       {
         "dtype": "float64",
         "name": "pct_counts_in_top_50_genes",
         "shape": [
-          5514
+          5561
         ],
         "type": "vector"
       },
       {
         "dtype": "float64",
         "name": "pct_counts_in_top_100_genes",
         "shape": [
-          5514
+          5561
         ],
         "type": "vector"
       },
       {
         "dtype": "float64",
         "name": "pct_counts_in_top_200_genes",
         "shape": [
-          5514
+          5561
         ],
         "type": "vector"
       },
       {
         "dtype": "float64",
         "name": "pct_counts_in_top_500_genes",
         "shape": [
-          5514
+          5561
         ],
         "type": "vector"
       },
       {
         "dtype": "int64",
         "name": "n_genes",
         "shape": [
-          5514
+          5561
         ],
         "type": "vector"
       },
       {
         "dtype": "float32",
         "name": "size_factors",
         "shape": [
-          5514
+          5561
         ],
         "type": "vector"
       }
@@ -134,7 +134,7 @@
         "dtype": "int64",
         "name": "spatial",
         "shape": [
-          5514,
+          5561,
           2
         ],
         "type": "densematrix"
@@ -236,79 +236,79 @@
         "name": "feature_id",
         "schema_type": "string",
         "shape": [
-          14015
+          14016
         ],
         "type": "vector"
       },
       {
         "dtype": "category",
         "name": "feature_types",
         "shape": [
-          14015
+          14016
         ],
         "type": "vector"
       },
       {
         "dtype": "category",
         "name": "genome",
         "shape": [
-          14015
+          14016
         ],
         "type": "vector"
       },
       {
         "dtype": "int64",
         "name": "n_cells_by_counts",
         "shape": [
-          14015
+          14016
         ],
         "type": "vector"
       },
       {
         "dtype": "float32",
         "name": "mean_counts",
         "shape": [
-          14015
+          14016
         ],
         "type": "vector"
       },
       {
         "dtype": "float32",
         "name": "log1p_mean_counts",
         "shape": [
-          14015
+          14016
         ],
         "type": "vector"
       },
       {
         "dtype": "float64",
         "name": "pct_dropout_by_counts",
         "shape": [
-          14015
+          14016
         ],
         "type": "vector"
       },
       {
         "dtype": "float32",
         "name": "total_counts",
         "shape": [
-          14015
+          14016
         ],
         "type": "vector"
       },
       {
         "dtype": "float32",
         "name": "log1p_total_counts",
         "shape": [
-          14015
+          14016
         ],
         "type": "vector"
       },
       {
         "dtype": "int64",
         "name": "n_cells",
         "shape": [
-          14015
+          14016
         ],
         "type": "vector"
       },
@@ -318,7 +318,7 @@
         "name": "feature_name",
         "schema_type": "string",
         "shape": [
-          14015
+          14016
         ],
         "type": "vector"
       }
@@ -328,14 +328,14 @@
   },
   "uns": {
     "dataset_description": "This dataset is provided as part of the Technical Note: Post-Xenium In Situ Applications: Immunofluorescence, H&E, and Visium CytAssist Spatial Gene Expression (CG000709). Post-Xenium samples were compared to controls (samples not processed through the Xenium workflow) using 5 \u00b5m (FFPE) serial sections.",
-    "dataset_id": "10x_datasets/human_colon_cancer_xenium",
-    "dataset_name": "10X Xenium - Human Colon",
+    "dataset_id": "tenx_visium/post_xenium/human_colon_cancer",
+    "dataset_name": "10X Post Xenium - Human Colon",
     "dataset_organism": "Homo sapiens",
     "dataset_reference": "10x2023colon",
     "dataset_summary": "Gene expression library of Post Xenium Human Colon Cancer (CytAssist FFPE) using the Human Whole Transcriptome Probe Set - Replicate 1",
     "dataset_url": "https://www.10xgenomics.com/datasets/visium-cytassist-gene-expression-libraries-of-post-xenium-human-colon-cancer-ffpe-using-the-human-whole-transcriptome-probe-set-2-standard",
-    "date_created": "20-08-2024",
-    "file_size": 86811935,
+    "date_created": "23-09-2024",
+    "file_size": 86834646,
     "normalization_id": "log_cp10k"
   }
 }
diff --git a/...human_brain_cancer_visium/data/state.yaml → ...xenium/human_colon_cancer/data/state.yaml b/...human_brain_cancer_visium/data/state.yaml → ...xenium/human_colon_cancer/data/state.yaml
diff --git a/...asets/human_colon_cancer_xenium/index.qmd → .../post_xenium/human_colon_cancer/index.qmd b/...asets/human_colon_cancer_xenium/index.qmd → .../post_xenium/human_colon_cancer/index.qmd
@@ -1,8 +1,8 @@
 ---
-dataset-id: "10x_datasets/human_colon_cancer_xenium"
-title: "10X Xenium - Human Colon"
+dataset-id: "tenx_visium/post_xenium/human_colon_cancer"
+title: "10X Post Xenium - Human Colon"
 subtitle: "Gene expression library of Post Xenium Human Colon Cancer (CytAssist FFPE) using the Human Whole Transcriptome Probe Set - Replicate 1"
-categories: ["10x_datasets"]
+categories: ["tenx_visium"]
 css: [/datasets/datasets.css]
 title-block-banner: transparent
 toc: false
@@ -12,8 +12,8 @@ citation-location: document
 
 ```{r}
 #| include: false
-params <- list(data_dir = "datasets/10x_datasets/human_colon_cancer_xenium/data", results_dir = "results")
-params <- list(data_dir = "./data", results_dir = "../../../results")
+params <- list(data_dir = "datasets/tenx_visium/post_xenium/human_colon_cancer/data", results_dir = "results")
+params <- list(data_dir = "./data", results_dir = "../../../../results")
 ```
 
 {{< include /datasets/_include/_index_template.qmd >}}