Tissue Short Codes Updates

docs/public/data_matrix_comparison.jsx

@@ -10,7 +10,7 @@
                 "query": {
                     "url": "/data_matrix_aggregations/?type=File&sample_summary.studies=Benchmarking&dataset!=No+value&dataset!=colo829blt_in_silico&dataset!=colo829_snv_indel_challenge_data&dataset!=mei_detection_challenge_data&dataset!=ipsc_snv_indel_challenge_data&status=open&status=open-early&status=open-network&status=protected&status=protected-early&status=protected-network&limit=all",
                     "columnAggFields": ["file_sets.libraries.assay.display_title", "sequencing.sequencer.platform"],
-                    "rowAggFields": ["donors.display_title", "sample_summary.tissues", "dataset", "data_type"]
+                    "rowAggFields": ["donors.display_title", "sample_summary.tissue_short_names", "dataset", "data_type"]
                 },
                 "resultItemPostProcessFuncKey": "cellLinePostProcess",
                 "resultTransformedPostProcessFuncKey": "dsaChainFile",
@@ -48,7 +48,7 @@
                 "query": {
                     "url": "/data_matrix_aggregations/?type=File&sample_summary.studies=Production&dataset!=No+value&status=open&status=open-early&status=open-network&status=protected&status=protected-early&status=protected-network&limit=all",
                     "columnAggFields": ["file_sets.libraries.assay.display_title", "sequencing.sequencer.platform"],
-                    "rowAggFields": ["donors.display_title", "sample_summary.tissues"]
+                    "rowAggFields": ["donors.display_title", "sample_summary.tissue_short_names"]
                 },
                 "headerFor": null,
                 "idLabel": "production"

src/encoded/item_utils/file.py

@@ -20,6 +20,36 @@
     get_property_values_from_identifiers,
 )
 
+# temporary mapping for tissue short names
+# to be used in tests until proper metadata implementation is done
+# the format will be: [TPC code] - [Portal facet]
+TPC_CODE_TO_FULL_NAME = {
+    "3A": "3A - Whole Blood",
+    "3B": "3B - Buccal Swab",
+    "3C": "3C - Esophagus",
+    "3E": "3E - Colon, Asc",
+    "3G": "3G - Colon, Desc",
+    "3I": "3I - Liver",
+    "3K": "3K - Adrenal Gland, L",
+    "3M": "3M - Adrenal Gland, R",
+    "3O": "3O - Aorta",
+    "3Q": "3Q - Lung",
+    "3S": "3S - Heart",
+    "3U": "3U - Testis, L",
+    "3W": "3W - Testis, R",
+    "3Y": "3Y - Ovary, L",
+    "3AA": "3AA - Ovary, R",
+    "3AC": "3AC - Fibroblast",
+    "3AD": "3AD - Skin, Calf",
+    "3AF": "3AF - Skin, Abdomen",
+    "3AH": "3AH - Muscle",
+    "3AK": "3AK - Brain, Frontal Lobe",
+    "3AL": "3AL - Brain, Temporal Lobe",
+    "3AM": "3AM - Brain, Cerebellum",
+    "3AN": "3AN - Brain, Hippocampus, L",
+    "3AO": "3AO - Brain, Hippocampus, R",
+}
+
 
 def get_file_format(properties: Dict[str, Any]) -> Union[str, Dict[str, Any]]:
     """Get file format from properties."""
@@ -485,4 +515,30 @@ def get_tissue_category(file: Dict[str, Any], request_handler: RequestHandler) -
         partial(
             tissue.get_category, request_handler=request_handler
         )
-    )
+    )
+
+def get_tissue_protocol_id(file: Dict[str, Any], request_handler: RequestHandler) -> List[str]:
+    """
+    Get tissue protocol ID from external ID.
+    """
+    return get_property_values_from_identifiers(
+        request_handler,
+        get_tissues(file, request_handler),
+        partial(
+            tissue.get_protocol_id
+        )
+    )
+
+def get_tissue_short_name(file: Dict[str, Any], request_handler: RequestHandler) -> List[str]:
+    """
+    Get tissue short name from protocol ID using temporary mapping.
+    """
+    protocol_ids = get_tissue_protocol_id(file, request_handler)
+    short_names = []
+    for pid in protocol_ids:
+        short_name = TPC_CODE_TO_FULL_NAME.get(pid)
+        if short_name:
+            short_names.append(short_name)
+        else:
+            short_names.append(pid)  # Fallback to protocol ID if not found
+    return short_names

src/encoded/schemas/file.json

@@ -337,7 +337,7 @@
             "title": "Donor Hardy Scale",
             "aggregation_type": "stats"
         },
-        "sample_summary.tissues": {
+        "sample_summary.tissue_short_names": {
             "title": "Tissue"
         },
         "file_sets.libraries.assay.display_title": {

src/encoded/static/components/util/Schemas.js

@@ -256,6 +256,7 @@ export const Field = {
         'file_format.display_title': 'File Format',
         'data_category': 'Data Category',
         'software.display_title': 'Software',
+        'sample_summary.tissue_subtypes': 'Subtype',
         '@id': 'Link',
         display_title: 'Title',
     },

src/encoded/static/components/util/data.js

@@ -5,38 +5,69 @@
 const germLayerTissueMapping = {
     Ectoderm: {
         values: [
-            'Brain',
-            'Brain - Cerebellum',
-            'Brain - Frontal lobe',
-            'Brain - Hippocampus',
-            'Brain - Temporal lobe',
-            'Skin',
-            'Skin - Abdomen (non-exposed)',
-            'Skin - Calf (sun-exposed)',
-            'Non-exposed Skin',
-            'Sun-exposed Skin',
+            "Brain",
+            "Brain, FL 3AK",
+            "Brain, TL 3AL",
+            "Brain, CB 3AM",
+            "Brain, HL 3AN",
+            "Brain, HR 3AO",
+            "Skin",
+            "Non-exposed Skin",
+            "Sun-exposed Skin",
+            "Skin, SE 3AD",
+            "Skin, NE 3AF",
         ],
     },
     Mesoderm: {
-        values: ['Aorta', 'Fibroblast', 'Heart', 'Muscle', 'Adrenal Gland'],
+        values: [
+            "Aorta",
+            "Aorta 3O",
+            "Fibroblast",
+            "Fibroblast 3AC",
+            "Heart",
+            "Heart 3S",
+            "Muscle",
+            "Muscle 3AH",
+            "Adrenal Gland",
+            "Adrenal Gland, L 3K",
+            "Adrenal Gland, R 3M",
+        ],
     },
     Endoderm: {
         values: [
-            'Colon',
-            'Colon - Ascending',
-            'Colon - Descending',
-            'Ascending Colon',
-            'Descending Colon',
-            'Esophagus',
-            'Liver',
-            'Lung',
+            "Colon",
+            "Colon - Ascending",
+            "Colon - Descending",
+            "Ascending Colon",
+            "Descending Colon",
+            "Colon, Asc 3E",
+            "Colon, Desc 3G",
+            "Esophagus",
+            "Esophagus 3C",
+            "Liver",
+            "Liver 3I",
+            "Lung",
+            "Lung 3Q",
         ],
     },
     'Germ cells': {
-        values: ['Ovary', 'Testis'],
+        values: [
+            "Ovary",
+            "Ovary, L 3Y",
+            "Ovary, R 3AA",
+            "Testis",
+            "Testis, L 3U",
+            "Testis, R 3W",
+        ],
     },
     'Clinically accessible': {
-        values: ['Blood', 'Buccal swab', 'Buccal Swab'],
+        values: [
+            "Blood",
+            "Blood 3A",
+            "Buccal swab",
+            "Buccal Swab",
+            "Buccal Swab 3B",
+        ],
     },
 };
 

src/encoded/static/components/viz/BarPlot/Chart.js

@@ -12,6 +12,22 @@ import { barplot_color_cycler } from './../ColorCycler';
 import { RotatedLabel } from './../components';
 import { PopoverViewContainer } from './ViewContainer';
 
+function shiftColor(color, delta = 0.1) {
+    const parsed = d3.color(color);
+    if (!parsed) return color;
+    const mixTarget = delta >= 0 ? 255 : 0;
+    const amount = Math.min(Math.abs(delta), 1);
+    parsed.r = Math.round(parsed.r + (mixTarget - parsed.r) * amount);
+    parsed.g = Math.round(parsed.g + (mixTarget - parsed.g) * amount);
+    parsed.b = Math.round(parsed.b + (mixTarget - parsed.b) * amount);
+    return parsed.formatHex();
+}
+
+function variantFromBaseColor(baseColor, index = 0) {
+    const deltas = [0, 0.12, -0.08, 0.18, -0.14];
+    return shiftColor(baseColor, deltas[index % deltas.length]);
+}
+
 
 /**
  * Return an object containing bar dimensions for first field which has more than 1 possible term, index of field used, and all fields passed originally.
@@ -131,7 +147,25 @@ export function genChartBarDims(
     _.forEach(barData.bars, function(bar){
         if (!Array.isArray(bar.bars)) return;
         _.forEach(bar.bars, function(b){
-            return _.extend(b, { 'color' : barplot_color_cycler.colorForNode(b) });
+            const baseColor = barplot_color_cycler.colorForNode(b);
+            _.extend(b, { 'color': baseColor, 'baseColor': baseColor });
+
+            if (Array.isArray(b.bars)) {
+                const sortedGrandChildren = b.bars.slice(0).sort(function(g1, g2){
+                    const g1Count = typeof g1[aggregateType] === 'number' ? g1[aggregateType] : g1.count || 0;
+                    const g2Count = typeof g2[aggregateType] === 'number' ? g2[aggregateType] : g2.count || 0;
+                    return g1Count - g2Count;
+                });
+                const len = sortedGrandChildren.length;
+                _.forEach(sortedGrandChildren, function(grandChild, idx) {
+                    // If only one secondary bucket, keep the exact primary color to stay in sync with the legend.
+                    const ratio = len > 1 ? idx / (len - 1) : 0;
+                    const delta = len > 1 ? (0.2 - (0.4 * ratio)) : 0;
+                    const variantColor = len > 1 ? shiftColor(baseColor, delta) : baseColor;
+                    _.extend(grandChild, { 'color': variantColor, 'baseColor': baseColor });
+                });
+                b.bars = sortedGrandChildren;
+            }
         });
     });