feat: dataset categories

configs/dmmm.yaml

@@ -42,12 +42,12 @@ algorithms:
 datasets:
   # TODO: use old paramaters for datasets
   # HIV: https://github.com/Reed-CompBio/spras-benchmarking/blob/0293ae4dc0be59502fac06b42cfd9796a4b4413e/hiv-benchmarking/spras-config/config.yaml
-  - label: dmmmhiv060
+  - label: dmmmhiv_060
     node_files: ["processed_prize_060.txt"]
     edge_files: ["../../../databases/irefindex/phosphosite-irefindex13.0-uniprot.txt"]
     other_files: []
     data_dir: "datasets/hiv/processed"
-  - label: dmmmhiv05
+  - label: dmmmhiv_05
     node_files: ["processed_prize_05.txt"]
     edge_files: ["../../../databases/irefindex/phosphosite-irefindex13.0-uniprot.txt"]
     other_files: []
@@ -58,21 +58,21 @@ datasets:
     edge_files: ["network1.txt"]
     other_files: []
     data_dir: "datasets/yeast-osmotic-stress/processed"
-  - label: dmmmalopecia_areata
+  - label: dmmmdiseases_alopecia_areata
     data_dir: datasets/diseases
     edge_files:
       - raw/string_interactome.txt
     node_files:
       - prize_files/alopecia_areata_prizes.txt
     other_files: []
-  - label: dmmmdiabetes_mellitus
+  - label: dmmmdiseases_diabetes_mellitus
     data_dir: datasets/diseases
     edge_files:
       - raw/string_interactome.txt
     node_files:
       - prize_files/diabetes_mellitus_prizes.txt
     other_files: []
-  - label: dmmmcellline_fadu
+  - label: dmmmdepmap_cellline_fadu
     data_dir: datasets/depmap
     edge_files: ["../../databases/irefindex/phosphosite-irefindex13.0-uniprot.txt"]
     node_files: ["processed/FADU_cell_line_prizes_input_nonzero.txt"]
@@ -81,12 +81,12 @@ gold_standards:
   - label: gs0
     node_files: ['GS_files/Alopecia_areata_GS.txt']
     data_dir: "datasets/diseases"
-    dataset_labels: ["dmmmalopecia_areata"]
+    dataset_labels: ["dmmmdiseases_alopecia_areata"]
   - label: gs1
     node_files: ['GS_files/Diabetes_mellitus_GS.txt']
     data_dir: "datasets/diseases"
-    dataset_labels: ["dmmmdiabetes_mellitus"]
+    dataset_labels: ["dmmmdiseases_diabetes_mellitus"]
   - label: gs_fadu
     node_files: ["processed/FADU_gold_standard.txt"]
     data_dir: datasets/depmap
-    dataset_labels: ["dmmmcellline_fadu"]
+    dataset_labels: ["dmmmdepmap_cellline_fadu"]

configs/pra.yaml

@@ -49,7 +49,7 @@ algorithms:
       include: true
 
 datasets:
-  - label: pramuscleskeletal2018
+  - label: prarn_muscleskeletal2018
     node_files: ["sources.txt", "targets.txt"]
     # DataLoader.py can currently only load a single edge file, which is the primary network
     edge_files: ["interactome.tsv"]

web/.prettierrc

@@ -0,0 +1,12 @@
+{
+  "printWidth": 120,
+  "plugins": ["prettier-plugin-astro"],
+  "overrides": [
+    {
+      "files": "*.astro",
+      "options": {
+        "parser": "astro"
+      }
+    }
+  ]
+}

web/astro.config.mts

@@ -1,8 +1,8 @@
 // @ts-check
-import { defineConfig } from 'astro/config';
+import { defineConfig } from "astro/config";
 
 // https://astro.build/config
 export default defineConfig({
-    base: '/spras-benchmarking',
-    trailingSlash: 'always'
+  base: "/spras-benchmarking",
+  trailingSlash: "always",
 });

web/package.json

@@ -3,21 +3,25 @@
   "type": "module",
   "version": "0.0.1",
   "scripts": {
-    "prepare-output": "mkdir -p public/data && cp -r ../output/ public/data",
+    "prepare-output": "mkdir -p public/data && cp -r ../output/ public/data && cp -r ../configs/ public/data",
     "dev": "pnpm prepare-output && astro dev",
     "build": "pnpm prepare-output && astro build",
     "preview": "astro preview",
-    "astro": "astro"
+    "astro": "astro",
+    "format": "pnpm exec prettier . --write"
   },
   "dependencies": {
     "@fontsource-variable/noto-sans": "^5.2.10",
     "astro": "^5.16.6",
     "dayjs": "^1.11.19",
     "medium-zoom": "^1.1.0",
-    "sass": "^1.97.1"
+    "sass": "^1.97.1",
+    "yaml": "^2.8.2"
   },
   "devDependencies": {
+    "prettier": "3.7.4",
+    "prettier-plugin-astro": "0.14.1",
     "vis-data": "^8.0.3",
     "vis-network": "^10.0.2"
   }
-}
+}

web/src/components/Colors.astro

@@ -1,18 +1,41 @@
 <style is:global lang="scss">
-    @use 'sass:color';
+  @use "sass:color";
 
-    $color-1: oklch(0.6744 0.1426 151.9);
-    $color-2: oklch(0.6376 0.2299 24.84);
-    $color-3: oklch(0.8002 0.1669 74.36);
-    $color-4: oklch(0.6465 0.1022 212.93);
+  $color-1: oklch(0.6744 0.1426 151.9);
+  $color-2: oklch(50.908% 0.1675 306.81);
+  $color-3: oklch(0.6376 0.2299 24.84);
+  $color-4: oklch(0.8002 0.1669 74.36);
+  $color-5: oklch(0.6465 0.1022 212.93);
 
-    .color-1 { color: color.adjust($color-1, $lightness: -20%); }
-    .color-2 { color: color.adjust($color-2, $lightness: -20%); }
-    .color-3 { color: color.adjust($color-3, $lightness: -20%); }
-    .color-4 { color: color.adjust($color-4, $lightness: -20%); }
+  .color-1 {
+    color: color.adjust($color-1, $lightness: -20%);
+  }
+  .color-2 {
+    color: color.adjust($color-2, $lightness: -20%);
+  }
+  .color-3 {
+    color: color.adjust($color-3, $lightness: -20%);
+  }
+  .color-4 {
+    color: color.adjust($color-4, $lightness: -20%);
+  }
+  .color-5 {
+    color: color.adjust($color-5, $lightness: -20%);
+  }
 
-    .color-1-dark { color: color.adjust($color-1, $lightness: -40%); }
-    .color-2-dark { color: color.adjust($color-2, $lightness: -40%); }
-    .color-3-dark { color: color.adjust($color-3, $lightness: -40%); }
-    .color-4-dark { color: color.adjust($color-4, $lightness: -40%); }
+  .color-1-dark {
+    color: color.adjust($color-1, $lightness: -40%);
+  }
+  .color-2-dark {
+    color: color.adjust($color-2, $lightness: -40%);
+  }
+  .color-3-dark {
+    color: color.adjust($color-3, $lightness: -40%);
+  }
+  .color-4-dark {
+    color: color.adjust($color-4, $lightness: -40%);
+  }
+  .color-5-dark {
+    color: color.adjust($color-5, $lightness: -40%);
+  }
 </style>

web/src/components/MediumZoom.astro

@@ -1,5 +1,5 @@
 <script>
-    import mediumZoom from 'medium-zoom';
+  import mediumZoom from "medium-zoom";
 
-    mediumZoom('[data-zoomable]')
+  mediumZoom("[data-zoomable]");
 </script>