@vitessce/biomarker-select 3.5.5 → 3.5.7

package/dist/index.js

@@ -910,7 +910,9 @@ const ViewType = {
   DOT_PLOT: "dotPlot",
   FEATURE_BAR_PLOT: "featureBarPlot",
   BIOMARKER_SELECT: "biomarkerSelect",
-  LINK_CONTROLLER: "linkController"
+  LINK_CONTROLLER: "linkController",
+  DUAL_SCATTERPLOT: "dualScatterplot",
+  TREEMAP: "treemap"
 };
 const AsyncFunctionType = {
   // String input (rather than Node input)
@@ -974,15 +976,23 @@ const CoordinationType = {
   HEATMAP_ZOOM_Y: "heatmapZoomY",
   HEATMAP_TARGET_X: "heatmapTargetX",
   HEATMAP_TARGET_Y: "heatmapTargetY",
-  OBS_FILTER: "obsFilter",
   OBS_HIGHLIGHT: "obsHighlight",
+  OBS_SELECTION: "obsSelection",
   OBS_SET_SELECTION: "obsSetSelection",
+  OBS_SELECTION_MODE: "obsSelectionMode",
+  OBS_FILTER: "obsFilter",
+  OBS_SET_FILTER: "obsSetFilter",
+  OBS_FILTER_MODE: "obsFilterMode",
   OBS_SET_HIGHLIGHT: "obsSetHighlight",
   OBS_SET_EXPANSION: "obsSetExpansion",
   OBS_SET_COLOR: "obsSetColor",
-  FEATURE_FILTER: "featureFilter",
   FEATURE_HIGHLIGHT: "featureHighlight",
   FEATURE_SELECTION: "featureSelection",
+  FEATURE_SET_SELECTION: "featureSetSelection",
+  FEATURE_SELECTION_MODE: "featureSelectionMode",
+  FEATURE_FILTER: "featureFilter",
+  FEATURE_SET_FILTER: "featureSetFilter",
+  FEATURE_FILTER_MODE: "featureFilterMode",
   FEATURE_VALUE_COLORMAP: "featureValueColormap",
   FEATURE_VALUE_TRANSFORM: "featureValueTransform",
   FEATURE_VALUE_COLORMAP_RANGE: "featureValueColormapRange",
@@ -1049,14 +1059,22 @@ const CoordinationType = {
   SPATIAL_CHANNEL_LABEL_SIZE: "spatialChannelLabelSize",
   // Multi-sample / comparative
   SAMPLE_TYPE: "sampleType",
+  SAMPLE_SELECTION: "sampleSelection",
   SAMPLE_SET_SELECTION: "sampleSetSelection",
+  SAMPLE_SELECTION_MODE: "sampleSelectionMode",
+  SAMPLE_FILTER: "sampleFilter",
+  SAMPLE_SET_FILTER: "sampleSetFilter",
+  SAMPLE_FILTER_MODE: "sampleFilterMode",
   SAMPLE_SET_COLOR: "sampleSetColor",
+  SAMPLE_HIGHLIGHT: "sampleHighlight",
   EMBEDDING_POINTS_VISIBLE: "embeddingPointsVisible",
   EMBEDDING_CONTOURS_VISIBLE: "embeddingContoursVisible",
   EMBEDDING_CONTOURS_FILLED: "embeddingContoursFilled",
   EMBEDDING_CONTOUR_PERCENTILES: "embeddingContourPercentiles",
   CONTOUR_COLOR_ENCODING: "contourColorEncoding",
-  CONTOUR_COLOR: "contourColor"
+  CONTOUR_COLOR: "contourColor",
+  // Treemap
+  HIERARCHY_LEVELS: "hierarchyLevels"
 };
 const COMPONENT_COORDINATION_TYPES = {
   [ViewType.SCATTERPLOT]: [
@@ -1081,6 +1099,50 @@ const COMPONENT_COORDINATION_TYPES = {
     CoordinationType.OBS_FILTER,
     CoordinationType.OBS_HIGHLIGHT,
     CoordinationType.OBS_SET_SELECTION,
+    CoordinationType.OBS_SET_FILTER,
+    CoordinationType.OBS_SET_HIGHLIGHT,
+    CoordinationType.OBS_SET_COLOR,
+    CoordinationType.FEATURE_HIGHLIGHT,
+    CoordinationType.FEATURE_SELECTION,
+    CoordinationType.FEATURE_VALUE_COLORMAP,
+    CoordinationType.FEATURE_VALUE_COLORMAP_RANGE,
+    CoordinationType.OBS_COLOR_ENCODING,
+    CoordinationType.ADDITIONAL_OBS_SETS,
+    CoordinationType.TOOLTIPS_VISIBLE,
+    CoordinationType.SAMPLE_TYPE,
+    CoordinationType.SAMPLE_SET_SELECTION,
+    CoordinationType.SAMPLE_SET_FILTER,
+    CoordinationType.SAMPLE_SET_COLOR,
+    CoordinationType.EMBEDDING_POINTS_VISIBLE,
+    CoordinationType.EMBEDDING_CONTOURS_VISIBLE,
+    CoordinationType.EMBEDDING_CONTOURS_FILLED,
+    CoordinationType.EMBEDDING_CONTOUR_PERCENTILES,
+    CoordinationType.CONTOUR_COLOR_ENCODING,
+    CoordinationType.CONTOUR_COLOR
+  ],
+  [ViewType.DUAL_SCATTERPLOT]: [
+    CoordinationType.DATASET,
+    CoordinationType.OBS_TYPE,
+    CoordinationType.FEATURE_TYPE,
+    CoordinationType.FEATURE_VALUE_TYPE,
+    CoordinationType.OBS_LABELS_TYPE,
+    CoordinationType.EMBEDDING_TYPE,
+    CoordinationType.EMBEDDING_ZOOM,
+    CoordinationType.EMBEDDING_ROTATION,
+    CoordinationType.EMBEDDING_TARGET_X,
+    CoordinationType.EMBEDDING_TARGET_Y,
+    CoordinationType.EMBEDDING_TARGET_Z,
+    CoordinationType.EMBEDDING_OBS_SET_POLYGONS_VISIBLE,
+    CoordinationType.EMBEDDING_OBS_SET_LABELS_VISIBLE,
+    CoordinationType.EMBEDDING_OBS_SET_LABEL_SIZE,
+    CoordinationType.EMBEDDING_OBS_RADIUS,
+    CoordinationType.EMBEDDING_OBS_RADIUS_MODE,
+    CoordinationType.EMBEDDING_OBS_OPACITY,
+    CoordinationType.EMBEDDING_OBS_OPACITY_MODE,
+    CoordinationType.OBS_FILTER,
+    CoordinationType.OBS_HIGHLIGHT,
+    CoordinationType.OBS_SET_SELECTION,
+    CoordinationType.OBS_SET_FILTER,
     CoordinationType.OBS_SET_HIGHLIGHT,
     CoordinationType.OBS_SET_COLOR,
     CoordinationType.FEATURE_HIGHLIGHT,
@@ -1092,6 +1154,7 @@ const COMPONENT_COORDINATION_TYPES = {
     CoordinationType.TOOLTIPS_VISIBLE,
     CoordinationType.SAMPLE_TYPE,
     CoordinationType.SAMPLE_SET_SELECTION,
+    CoordinationType.SAMPLE_SET_FILTER,
     CoordinationType.SAMPLE_SET_COLOR,
     CoordinationType.EMBEDDING_POINTS_VISIBLE,
     CoordinationType.EMBEDDING_CONTOURS_VISIBLE,
@@ -1158,6 +1221,7 @@ const COMPONENT_COORDINATION_TYPES = {
     CoordinationType.OBS_FILTER,
     CoordinationType.OBS_HIGHLIGHT,
     CoordinationType.OBS_SET_SELECTION,
+    CoordinationType.OBS_SET_FILTER,
     CoordinationType.OBS_SET_HIGHLIGHT,
     CoordinationType.OBS_SET_COLOR,
     CoordinationType.FEATURE_HIGHLIGHT,
@@ -1194,6 +1258,7 @@ const COMPONENT_COORDINATION_TYPES = {
     CoordinationType.OBS_FILTER,
     CoordinationType.OBS_HIGHLIGHT,
     CoordinationType.OBS_SET_SELECTION,
+    CoordinationType.OBS_SET_FILTER,
     CoordinationType.OBS_SET_HIGHLIGHT,
     CoordinationType.OBS_SET_COLOR,
     CoordinationType.FEATURE_HIGHLIGHT,
@@ -1253,6 +1318,7 @@ const COMPONENT_COORDINATION_TYPES = {
     CoordinationType.OBS_FILTER,
     CoordinationType.OBS_HIGHLIGHT,
     CoordinationType.OBS_SET_SELECTION,
+    CoordinationType.OBS_SET_FILTER,
     CoordinationType.OBS_SET_HIGHLIGHT,
     CoordinationType.OBS_SET_COLOR,
     CoordinationType.FEATURE_FILTER,
@@ -1268,6 +1334,7 @@ const COMPONENT_COORDINATION_TYPES = {
     CoordinationType.DATASET,
     CoordinationType.OBS_TYPE,
     CoordinationType.OBS_SET_SELECTION,
+    CoordinationType.OBS_SET_FILTER,
     CoordinationType.OBS_SET_EXPANSION,
     CoordinationType.OBS_SET_HIGHLIGHT,
     CoordinationType.OBS_SET_COLOR,
@@ -1279,6 +1346,7 @@ const COMPONENT_COORDINATION_TYPES = {
     CoordinationType.DATASET,
     CoordinationType.OBS_TYPE,
     CoordinationType.OBS_SET_SELECTION,
+    CoordinationType.OBS_SET_FILTER,
     CoordinationType.OBS_SET_EXPANSION,
     CoordinationType.OBS_SET_HIGHLIGHT,
     CoordinationType.OBS_SET_COLOR,
@@ -1311,6 +1379,7 @@ const COMPONENT_COORDINATION_TYPES = {
     CoordinationType.FEATURE_VALUE_TRANSFORM,
     CoordinationType.FEATURE_VALUE_TRANSFORM_COEFFICIENT,
     CoordinationType.OBS_SET_SELECTION,
+    CoordinationType.OBS_SET_FILTER,
     CoordinationType.OBS_SET_HIGHLIGHT,
     CoordinationType.OBS_SET_COLOR,
     CoordinationType.ADDITIONAL_OBS_SETS,
@@ -1327,7 +1396,8 @@ const COMPONENT_COORDINATION_TYPES = {
     CoordinationType.ADDITIONAL_OBS_SETS,
     CoordinationType.OBS_SET_COLOR,
     CoordinationType.OBS_COLOR_ENCODING,
-    CoordinationType.OBS_SET_SELECTION
+    CoordinationType.OBS_SET_SELECTION,
+    CoordinationType.OBS_SET_FILTER
   ],
   [ViewType.LAYER_CONTROLLER]: [
     CoordinationType.DATASET,
@@ -1442,11 +1512,13 @@ const COMPONENT_COORDINATION_TYPES = {
     CoordinationType.FEATURE_VALUE_POSITIVITY_THRESHOLD,
     CoordinationType.FEATURE_VALUE_COLORMAP,
     CoordinationType.OBS_SET_SELECTION,
+    CoordinationType.OBS_SET_FILTER,
     CoordinationType.OBS_SET_HIGHLIGHT,
     CoordinationType.OBS_SET_COLOR,
     CoordinationType.ADDITIONAL_OBS_SETS,
     CoordinationType.SAMPLE_TYPE,
     CoordinationType.SAMPLE_SET_SELECTION,
+    CoordinationType.SAMPLE_SET_FILTER,
     CoordinationType.SAMPLE_SET_COLOR
   ],
   higlass: [
@@ -1477,8 +1549,37 @@ const COMPONENT_COORDINATION_TYPES = {
   [ViewType.LINK_CONTROLLER]: [],
   [ViewType.BIOMARKER_SELECT]: [
     CoordinationType.FEATURE_SELECTION,
-    CoordinationType.SAMPLE_SET_SELECTION
+    CoordinationType.SAMPLE_SET_SELECTION,
+    CoordinationType.SAMPLE_SET_FILTER,
+    CoordinationType.OBS_SET_SELECTION,
+    CoordinationType.OBS_SET_FILTER
     // TODO: create coordination types for internal state of the biomarker selection view?
+  ],
+  [ViewType.TREEMAP]: [
+    CoordinationType.DATASET,
+    CoordinationType.OBS_TYPE,
+    CoordinationType.FEATURE_TYPE,
+    CoordinationType.FEATURE_VALUE_TYPE,
+    CoordinationType.OBS_FILTER,
+    CoordinationType.OBS_HIGHLIGHT,
+    CoordinationType.OBS_SET_SELECTION,
+    CoordinationType.OBS_SET_FILTER,
+    CoordinationType.OBS_SELECTION,
+    CoordinationType.OBS_SELECTION_MODE,
+    CoordinationType.OBS_SET_HIGHLIGHT,
+    CoordinationType.OBS_SET_COLOR,
+    CoordinationType.OBS_COLOR_ENCODING,
+    CoordinationType.ADDITIONAL_OBS_SETS,
+    CoordinationType.SAMPLE_TYPE,
+    CoordinationType.SAMPLE_SET_SELECTION,
+    CoordinationType.SAMPLE_SET_FILTER,
+    CoordinationType.SAMPLE_SET_COLOR,
+    CoordinationType.SAMPLE_SELECTION,
+    CoordinationType.SAMPLE_SELECTION_MODE,
+    CoordinationType.SAMPLE_FILTER,
+    CoordinationType.SAMPLE_FILTER_MODE,
+    CoordinationType.SAMPLE_HIGHLIGHT,
+    CoordinationType.HIERARCHY_LEVELS
   ]
 };
 var common = {
@@ -30871,8 +30972,8 @@ function BiomarkerSelectSubscriber(props) {
     coordinationScopes
   );
   const viewConfigStoreApi = useViewConfigStoreApi();
-  useViewConfig();
-  useSetViewConfig(viewConfigStoreApi);
+  const viewConfig = useViewConfig();
+  const setViewConfig = useSetViewConfig(viewConfigStoreApi);
   const [isSelecting, setIsSelecting] = useState(true);
   const [mode, setMode] = useState(null);
   const [step, setStep] = useState(null);
@@ -30906,7 +31007,20 @@ function BiomarkerSelectSubscriber(props) {
       getEdges,
       stratifications: stratificationOptions,
       onFinish: () => {
-        console.log("Done selecting");
+        setViewConfig({
+          ...viewConfig,
+          coordinationSpace: {
+            ...viewConfig.coordinationSpace,
+            sampleSetFilter: {
+              ...viewConfig.coordinationSpace.sampleSetFilter,
+              "case-control": currentStratificationSelection == null ? void 0 : currentStratificationSelection.sampleSets
+            },
+            sampleSetSelection: {
+              ...viewConfig.coordinationSpace.sampleSetSelection,
+              "case-control": currentStratificationSelection == null ? void 0 : currentStratificationSelection.sampleSets
+            }
+          }
+        });
       }
     }
   ) : null });

package/dist-tsc/BiomarkerSelectSubscriber.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"BiomarkerSelectSubscriber.d.ts","sourceRoot":"","sources":["../src/BiomarkerSelectSubscriber.js"],"names":[],"mappings":"AAcA;;;;;GAKG;AACH,iDAHG;IAA+F,qBAAqB,EAA5G;QAAE,IAAI,EAAE,MAAM,CAAC;QAAC,kBAAkB,EAAE,MAAM,CAAC;QAAC,UAAU,EAAE,CAAC,MAAM,EAAE,EAAE,MAAM,EAAE,CAAC,CAAA;KAAC,EAAE;CACvF,eAwFF"}
+{"version":3,"file":"BiomarkerSelectSubscriber.d.ts","sourceRoot":"","sources":["../src/BiomarkerSelectSubscriber.js"],"names":[],"mappings":"AAcA;;;;;GAKG;AACH,iDAHG;IAA+F,qBAAqB,EAA5G;QAAE,IAAI,EAAE,MAAM,CAAC;QAAC,kBAAkB,EAAE,MAAM,CAAC;QAAC,UAAU,EAAE,CAAC,MAAM,EAAE,EAAE,MAAM,EAAE,CAAC,CAAA;KAAC,EAAE;CACvF,eAmFF"}

package/dist-tsc/BiomarkerSelectSubscriber.js

@@ -30,24 +30,19 @@ export function BiomarkerSelectSubscriber(props) {
     const autocompleteNode = useCallback(async (inputValue) => autocompleteFeature(inputValue), [autocompleteFeature]);
     const getEdges = useCallback(async (node, targetModality) => transformFeature(node, targetModality), [transformFeature]);
     return (_jsx(_Fragment, { children: isSelecting ? (_jsx(ScmdUi, { mode: mode, setMode: setMode, step: step, setStep: setStep, currentModalityAgnosticSelection: currentModalityAgnosticSelection, setCurrentModalityAgnosticSelection: setCurrentModalityAgnosticSelection, currentModalitySpecificSelection: currentModalitySpecificSelection, setCurrentModalitySpecificSelection: setCurrentModalitySpecificSelection, currentStratificationSelection: currentStratificationSelection, setCurrentStratificationSelection: setCurrentStratificationSelection, autocompleteNode: autocompleteNode, getEdges: getEdges, stratifications: stratificationOptions, onFinish: () => {
-                // eslint-disable-next-line no-console
-                console.log('Done selecting');
-                /*
-                console.log(viewConfig);
                 setViewConfig({
-                  ...viewConfig,
-                  coordinationSpace: {
-                    ...viewConfig.coordinationSpace,
-                    sampleSetFilter: {
-                      ...viewConfig.coordinationSpace.sampleSetFilter,
-                      'case-control': currentStratificationSelection?.sampleSets,
+                    ...viewConfig,
+                    coordinationSpace: {
+                        ...viewConfig.coordinationSpace,
+                        sampleSetFilter: {
+                            ...viewConfig.coordinationSpace.sampleSetFilter,
+                            'case-control': currentStratificationSelection?.sampleSets,
+                        },
+                        sampleSetSelection: {
+                            ...viewConfig.coordinationSpace.sampleSetSelection,
+                            'case-control': currentStratificationSelection?.sampleSets,
+                        },
                     },
-                    sampleSetSelection: {
-                      ...viewConfig.coordinationSpace.sampleSetSelection,
-                      'case-control': currentStratificationSelection?.sampleSets,
-                    },
-                  },
                 });
-                */
             } })) : null }));
 }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@vitessce/biomarker-select",
-  "version": "3.5.5",
+  "version": "3.5.7",
   "author": "Gehlenborg Lab",
   "homepage": "http://vitessce.io",
   "repository": {
@@ -24,9 +24,9 @@
     "react-window": "^1.8.10",
     "fuse.js": "^7.0.0",
     "d3-dsv": "^1.1.1",
-    "@vitessce/constants-internal": "3.5.5",
-    "@vitessce/vit-s": "3.5.5",
-    "@vitessce/types": "3.5.5"
+    "@vitessce/constants-internal": "3.5.7",
+    "@vitessce/vit-s": "3.5.7",
+    "@vitessce/types": "3.5.7"
   },
   "devDependencies": {
     "@testing-library/jest-dom": "^5.16.4",

package/src/BiomarkerSelectSubscriber.js

@@ -80,10 +80,6 @@ export function BiomarkerSelectSubscriber(props) {
           getEdges={getEdges}
           stratifications={stratificationOptions}
           onFinish={() => {
-            // eslint-disable-next-line no-console
-            console.log('Done selecting');
-            /*
-            console.log(viewConfig);
             setViewConfig({
               ...viewConfig,
               coordinationSpace: {
@@ -98,7 +94,6 @@ export function BiomarkerSelectSubscriber(props) {
                 },
               },
             });
-            */
           }}
         />
       ) : null}