@haniffalab/cherita-react 1.4.1-dev.2025-10-20.528e0f75 → 1.4.1-dev.2025-10-22.61540191

package/dist/cjs/components/dotplot/Dotplot.js

@@ -4,7 +4,7 @@ Object.defineProperty(exports, "__esModule", {
   value: true
 });
 exports.Dotplot = Dotplot;
-var _react = _interopRequireWildcard(require("react"));
+var _react = require("react");
 var _lodash = _interopRequireDefault(require("lodash"));
 var _reactBootstrap = require("react-bootstrap");
 var _reactPlotly = _interopRequireDefault(require("react-plotly.js"));
@@ -15,9 +15,9 @@ var _SettingsContext = require("../../context/SettingsContext");
 var _LoadingIndicators = require("../../utils/LoadingIndicators");
 var _requests = require("../../utils/requests");
 var _Resolver = require("../../utils/Resolver");
+var _PlotAlert = require("../full-page/PlotAlert");
 var _Toolbar = require("../toolbar/Toolbar");
 function _interopRequireDefault(e) { return e && e.__esModule ? e : { default: e }; }
-function _interopRequireWildcard(e, t) { if ("function" == typeof WeakMap) var r = new WeakMap(), n = new WeakMap(); return (_interopRequireWildcard = function (e, t) { if (!t && e && e.__esModule) return e; var o, i, f = { __proto__: null, default: e }; if (null === e || "object" != typeof e && "function" != typeof e) return f; if (o = t ? n : r) { if (o.has(e)) return o.get(e); o.set(e, f); } for (const t in e) "default" !== t && {}.hasOwnProperty.call(e, t) && ((i = (o = Object.defineProperty) && Object.getOwnPropertyDescriptor(e, t)) && (i.get || i.set) ? o(f, t, i) : f[t] = e[t]); return f; })(e, t); }
 function ownKeys(e, r) { var t = Object.keys(e); if (Object.getOwnPropertySymbols) { var o = Object.getOwnPropertySymbols(e); r && (o = o.filter(function (r) { return Object.getOwnPropertyDescriptor(e, r).enumerable; })), t.push.apply(t, o); } return t; }
 function _objectSpread(e) { for (var r = 1; r < arguments.length; r++) { var t = null != arguments[r] ? arguments[r] : {}; r % 2 ? ownKeys(Object(t), !0).forEach(function (r) { _defineProperty(e, r, t[r]); }) : Object.getOwnPropertyDescriptors ? Object.defineProperties(e, Object.getOwnPropertyDescriptors(t)) : ownKeys(Object(t)).forEach(function (r) { Object.defineProperty(e, r, Object.getOwnPropertyDescriptor(t, r)); }); } return e; }
 function _defineProperty(e, r, t) { return (r = _toPropertyKey(r)) in e ? Object.defineProperty(e, r, { value: t, enumerable: !0, configurable: !0, writable: !0 }) : e[r] = t, e; }
@@ -30,7 +30,9 @@ function Dotplot(_ref) {
     showCtrlsBtn = false,
     setShowObs,
     setShowVars,
-    setShowControls
+    setShowControls,
+    plotType,
+    setPlotType
   } = _ref;
   const ENDPOINT = "dotplot";
   const dataset = (0, _DatasetContext.useDataset)();
@@ -142,9 +144,9 @@ function Dotplot(_ref) {
   const modeBarButtons = customModeBarButtons.length ? [customModeBarButtons, _constants.PLOTLY_MODEBAR_BUTTONS] : [_constants.PLOTLY_MODEBAR_BUTTONS];
   if (!serverError) {
     if (hasSelections) {
-      return /*#__PURE__*/_react.default.createElement("div", {
+      return /*#__PURE__*/React.createElement("div", {
         className: "cherita-plot cherita-dotplot position-relative"
-      }, isPending && /*#__PURE__*/_react.default.createElement(_LoadingIndicators.LoadingSpinner, null), /*#__PURE__*/_react.default.createElement(_reactPlotly.default, {
+      }, isPending && /*#__PURE__*/React.createElement(_LoadingIndicators.LoadingSpinner, null), /*#__PURE__*/React.createElement(_reactPlotly.default, {
         data: data,
         layout: layout,
         useResizeHandler: true,
@@ -158,22 +160,28 @@ function Dotplot(_ref) {
         }
       }));
     }
-    return /*#__PURE__*/_react.default.createElement("div", {
-      className: "cherita-dotplot"
-    }, /*#__PURE__*/_react.default.createElement(_reactBootstrap.Alert, {
-      variant: "light"
-    }, "Select", " ", showVarsBtn ? /*#__PURE__*/_react.default.createElement(_reactBootstrap.Button, {
+    return /*#__PURE__*/React.createElement(_PlotAlert.PlotAlert, {
+      variant: "info",
+      heading: "Dotplot",
+      plotType: plotType,
+      setPlotType: setPlotType
+    }, /*#__PURE__*/React.createElement("p", {
+      className: "p-0 m-0"
+    }, "Select one or more", " ", showVarsBtn ? /*#__PURE__*/React.createElement(_reactBootstrap.Button, {
       variant: "link",
       className: "border-0 p-0 align-baseline",
       onClick: setShowVars
-    }, "features") : "features", " ", "and a", " ", showObsBtn ? /*#__PURE__*/_react.default.createElement(_reactBootstrap.Button, {
+    }, "features") : "features", " ", "to display their expression across groups, then choose a", " ", showObsBtn ? /*#__PURE__*/React.createElement(_reactBootstrap.Button, {
       variant: "link",
       className: "border-0 p-0 align-baseline",
       onClick: setShowObs
-    }, "category") : "category"));
+    }, "category") : "category", " ", "to group observations in the dotplot."));
   } else {
-    return /*#__PURE__*/_react.default.createElement("div", null, /*#__PURE__*/_react.default.createElement(_reactBootstrap.Alert, {
-      variant: "danger"
-    }, serverError.message));
+    return /*#__PURE__*/React.createElement(_PlotAlert.PlotAlert, {
+      variant: "danger",
+      heading: "Dotplot",
+      plotType: plotType,
+      setPlotType: setPlotType
+    }, serverError.message || "An unexpected error occurred while generating the plot.");
   }
 }

package/dist/cjs/components/full-page/FullPage.js

@@ -4,7 +4,7 @@ Object.defineProperty(exports, "__esModule", {
   value: true
 });
 exports.FullPage = FullPage;
-var _react = _interopRequireWildcard(require("react"));
+var _react = require("react");
 var _material = require("@mui/material");
 var _reactBootstrap = require("react-bootstrap");
 var _constants = require("../../constants/constants");
@@ -27,7 +27,6 @@ var _VarList = require("../var-list/VarList");
 var _Violin = require("../violin/Violin");
 var _ViolinControls = require("../violin/ViolinControls");
 const _excluded = ["searchDiseases", "defaultPlotType"];
-function _interopRequireWildcard(e, t) { if ("function" == typeof WeakMap) var r = new WeakMap(), n = new WeakMap(); return (_interopRequireWildcard = function (e, t) { if (!t && e && e.__esModule) return e; var o, i, f = { __proto__: null, default: e }; if (null === e || "object" != typeof e && "function" != typeof e) return f; if (o = t ? n : r) { if (o.has(e)) return o.get(e); o.set(e, f); } for (const t in e) "default" !== t && {}.hasOwnProperty.call(e, t) && ((i = (o = Object.defineProperty) && Object.getOwnPropertyDescriptor(e, t)) && (i.get || i.set) ? o(f, t, i) : f[t] = e[t]); return f; })(e, t); }
 function _extends() { return _extends = Object.assign ? Object.assign.bind() : function (n) { for (var e = 1; e < arguments.length; e++) { var t = arguments[e]; for (var r in t) ({}).hasOwnProperty.call(t, r) && (n[r] = t[r]); } return n; }, _extends.apply(null, arguments); }
 function _objectWithoutProperties(e, t) { if (null == e) return {}; var o, r, i = _objectWithoutPropertiesLoose(e, t); if (Object.getOwnPropertySymbols) { var n = Object.getOwnPropertySymbols(e); for (r = 0; r < n.length; r++) o = n[r], -1 === t.indexOf(o) && {}.propertyIsEnumerable.call(e, o) && (i[o] = e[o]); } return i; }
 function _objectWithoutPropertiesLoose(r, e) { if (null == r) return {}; var t = {}; for (var n in r) if ({}.hasOwnProperty.call(r, n)) { if (-1 !== e.indexOf(n)) continue; t[n] = r[n]; } return t; }
@@ -55,6 +54,7 @@ function FullPage(_ref) {
   const XlBreakpoint = (0, _material.useMediaQuery)(_constants.BREAKPOINTS.XL);
   const showObsBtn = LgBreakpoint;
   const showVarsBtn = XlBreakpoint;
+  const showPlotBtn = showVarsBtn;
   const {
     plotControls,
     varMode,
@@ -91,85 +91,87 @@ function FullPage(_ref) {
       showObsBtn,
       showVarsBtn,
       showCtrlsBtn: true,
+      plotType,
       setShowObs,
       setShowVars,
-      setShowControls
+      setShowControls,
+      setPlotType
     };
     switch (plotType) {
       case _constants.PLOT_TYPES.DOTPLOT:
-        return /*#__PURE__*/_react.default.createElement(_Dotplot.Dotplot, commonProps);
+        return /*#__PURE__*/React.createElement(_Dotplot.Dotplot, commonProps);
       case _constants.PLOT_TYPES.MATRIXPLOT:
-        return /*#__PURE__*/_react.default.createElement(_Matrixplot.Matrixplot, commonProps);
+        return /*#__PURE__*/React.createElement(_Matrixplot.Matrixplot, commonProps);
       case _constants.PLOT_TYPES.HEATMAP:
-        return /*#__PURE__*/_react.default.createElement(_Heatmap.Heatmap, commonProps);
+        return /*#__PURE__*/React.createElement(_Heatmap.Heatmap, commonProps);
       case _constants.PLOT_TYPES.VIOLINPLOT:
-        return /*#__PURE__*/_react.default.createElement(_Violin.Violin, _extends({
+        return /*#__PURE__*/React.createElement(_Violin.Violin, _extends({
           mode: _constants.VIOLIN_MODES.MULTIKEY
         }, commonProps));
       case _constants.PLOT_TYPES.SCATTERPLOT:
       default:
-        return /*#__PURE__*/_react.default.createElement(_Scatterplot.Scatterplot, _extends({}, commonProps, {
+        return /*#__PURE__*/React.createElement(_Scatterplot.Scatterplot, _extends({}, commonProps, {
           isFullscreen: true
         }));
     }
   }, [plotType, showObsBtn, showVarsBtn]);
-  return /*#__PURE__*/_react.default.createElement("div", {
+  return /*#__PURE__*/React.createElement("div", {
     className: "cherita-app"
-  }, /*#__PURE__*/_react.default.createElement(_DatasetContext.DatasetProvider, props, /*#__PURE__*/_react.default.createElement(_reactBootstrap.Container, {
+  }, /*#__PURE__*/React.createElement(_DatasetContext.DatasetProvider, props, /*#__PURE__*/React.createElement(_reactBootstrap.Container, {
     fluid: true,
     className: "cherita-app-container"
-  }, /*#__PURE__*/_react.default.createElement("div", {
+  }, /*#__PURE__*/React.createElement("div", {
     className: "cherita-app-obs modern-scrollbars border-end h-100"
-  }, /*#__PURE__*/_react.default.createElement(_ObsList.ObsColsList, _extends({}, props, {
+  }, /*#__PURE__*/React.createElement(_ObsList.ObsColsList, _extends({}, props, {
     showSelectedAsActive: showSelectedAsActive,
     showHistograms: varMode === _constants.SELECTION_MODES.SINGLE,
     showColor: varMode === _constants.SELECTION_MODES.SINGLE
-  }))), /*#__PURE__*/_react.default.createElement("div", {
+  }))), /*#__PURE__*/React.createElement("div", {
     className: "cherita-app-canvas"
-  }, plot), /*#__PURE__*/_react.default.createElement("div", {
+  }, plot), /*#__PURE__*/React.createElement("div", {
     className: "cherita-app-sidebar p-3"
-  }, /*#__PURE__*/_react.default.createElement(_reactBootstrap.Card, null, /*#__PURE__*/_react.default.createElement(_reactBootstrap.Card.Body, null, /*#__PURE__*/_react.default.createElement("div", {
-    className: "sidebar-plotselector"
-  }, /*#__PURE__*/_react.default.createElement(_PlotTypeSelector.PlotTypeSelector, {
+  }, /*#__PURE__*/React.createElement(_reactBootstrap.Card, null, /*#__PURE__*/React.createElement(_reactBootstrap.Card.Body, null, /*#__PURE__*/React.createElement("div", {
+    className: "plotselector"
+  }, /*#__PURE__*/React.createElement(_PlotTypeSelector.PlotTypeSelector, {
     currentType: plotType,
     onChange: type => setPlotType(type)
-  })), plotType === _constants.PLOT_TYPES.SCATTERPLOT && isPseudospatial ? /*#__PURE__*/_react.default.createElement("div", {
+  })), plotType === _constants.PLOT_TYPES.SCATTERPLOT && isPseudospatial ? /*#__PURE__*/React.createElement("div", {
     className: "sidebar-pseudospatial"
-  }, /*#__PURE__*/_react.default.createElement(_Pseudospatial.Pseudospatial, {
+  }, /*#__PURE__*/React.createElement(_Pseudospatial.Pseudospatial, {
     plotType: pseudospatialPlotType,
     setPlotType: setpseudospatialPlotType,
     setShowControls: setShowPseudospatialControls
-  })) : /*#__PURE__*/_react.default.createElement(_react.default.Fragment, null), /*#__PURE__*/_react.default.createElement("div", {
+  })) : /*#__PURE__*/React.createElement(React.Fragment, null), /*#__PURE__*/React.createElement("div", {
     className: "sidebar-features"
-  }, /*#__PURE__*/_react.default.createElement(_SearchBar.SearchBar, {
+  }, /*#__PURE__*/React.createElement(_SearchBar.SearchBar, {
     searchDiseases: searchDiseases,
     searchVar: true
-  }), /*#__PURE__*/_react.default.createElement("div", {
+  }), /*#__PURE__*/React.createElement("div", {
     className: "sidebar-features-list"
-  }, /*#__PURE__*/_react.default.createElement(_VarList.VarNamesList, {
+  }, /*#__PURE__*/React.createElement(_VarList.VarNamesList, {
     mode: varMode
-  }))))))), /*#__PURE__*/_react.default.createElement("div", null, /*#__PURE__*/_react.default.createElement(_reactBootstrap.Modal, {
+  }))))))), /*#__PURE__*/React.createElement("div", null, /*#__PURE__*/React.createElement(_reactBootstrap.Modal, {
     show: showModal,
     onHide: () => setShowModal(false),
     centered: true
-  }, /*#__PURE__*/_react.default.createElement(_reactBootstrap.Modal.Header, {
+  }, /*#__PURE__*/React.createElement(_reactBootstrap.Modal.Header, {
     closeButton: true
-  }), /*#__PURE__*/_react.default.createElement(_reactBootstrap.Modal.Body, null)), /*#__PURE__*/_react.default.createElement(_offcanvas.OffcanvasObs, _extends({}, props, {
+  }), /*#__PURE__*/React.createElement(_reactBootstrap.Modal.Body, null)), /*#__PURE__*/React.createElement(_offcanvas.OffcanvasObs, _extends({}, props, {
     showSelectedAsActive: showSelectedAsActive,
     show: showObs,
     handleClose: () => setShowObs(false)
-  })), /*#__PURE__*/_react.default.createElement(_offcanvas.OffcanvasVars, {
+  })), /*#__PURE__*/React.createElement(_offcanvas.OffcanvasVars, {
     show: showVars,
     handleClose: () => setShowVars(false),
     mode: varMode
-  }), plotControls && /*#__PURE__*/_react.default.createElement(_offcanvas.OffcanvasControls, {
+  }), plotControls && /*#__PURE__*/React.createElement(_offcanvas.OffcanvasControls, {
     show: showControls,
     handleClose: () => setShowControls(false),
     Controls: plotControls
-  }), /*#__PURE__*/_react.default.createElement(_offcanvas.OffcanvasObsm, {
+  }), /*#__PURE__*/React.createElement(_offcanvas.OffcanvasObsm, {
     show: showObsm,
     handleClose: () => setShowObsm(false)
-  }), /*#__PURE__*/_react.default.createElement(_offcanvas.OffcanvasControls, {
+  }), /*#__PURE__*/React.createElement(_offcanvas.OffcanvasControls, {
     show: showPseudospatialControls,
     handleClose: () => setShowPseudospatialControls(false),
     Controls: _PseudospatialToolbar.PseudospatialToolbar,

package/dist/cjs/components/full-page/PlotAlert.js

@@ -0,0 +1,36 @@
+"use strict";
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports.PlotAlert = PlotAlert;
+var _material = require("@mui/material");
+var _reactBootstrap = require("react-bootstrap");
+var _constants = require("../../constants/constants");
+var _PlotTypeSelector = require("./PlotTypeSelector");
+function PlotAlert(_ref) {
+  let {
+    variant = "warning",
+    plotType = _constants.PLOT_TYPES.SCATTERPLOT,
+    setPlotType,
+    heading,
+    children
+  } = _ref;
+  const XlBreakpoint = (0, _material.useMediaQuery)(_constants.BREAKPOINTS.XL);
+  const showPlotSelector = XlBreakpoint;
+  return /*#__PURE__*/React.createElement(React.Fragment, null, showPlotSelector && /*#__PURE__*/React.createElement("div", {
+    className: "plotselector"
+  }, /*#__PURE__*/React.createElement(_PlotTypeSelector.PlotTypeSelector, {
+    currentType: plotType,
+    onChange: type => {
+      if (setPlotType) setPlotType(type);
+    }
+  })), /*#__PURE__*/React.createElement("div", {
+    className: "cherita-plot-alert h-100"
+  }, /*#__PURE__*/React.createElement("div", {
+    className: "w-100 h-100 d-flex justify-content-center align-items-center"
+  }, /*#__PURE__*/React.createElement(_reactBootstrap.Alert, {
+    variant: variant,
+    className: "m-0 w-75 w-lg-50 text-center"
+  }, heading && /*#__PURE__*/React.createElement(_reactBootstrap.Alert.Heading, null, heading), " ", children))));
+}

package/dist/cjs/components/full-page/PlotTypeSelector.js

@@ -4,54 +4,92 @@ Object.defineProperty(exports, "__esModule", {
   value: true
 });
 exports.PlotTypeSelector = PlotTypeSelector;
-var _react = _interopRequireDefault(require("react"));
-var _dotplot = _interopRequireDefault(require("../../../assets/images/plots/dotplot.svg"));
-var _heatmap = _interopRequireDefault(require("../../../assets/images/plots/heatmap.svg"));
-var _matrixplot = _interopRequireDefault(require("../../../assets/images/plots/matrixplot.svg"));
-var _scatterplot = _interopRequireDefault(require("../../../assets/images/plots/scatterplot.svg"));
-var _violin = _interopRequireDefault(require("../../../assets/images/plots/violin.svg"));
+var _react = require("react");
 var _constants = require("../../constants/constants");
+var _StyledTooltip = require("../../utils/StyledTooltip");
+var _DotPlotIcon = _interopRequireDefault(require("../icons/DotPlotIcon"));
+var _HeatmapIcon = _interopRequireDefault(require("../icons/HeatmapIcon"));
+var _MatrixPlotIcon = _interopRequireDefault(require("../icons/MatrixPlotIcon"));
+var _ScatterplotIcon = _interopRequireDefault(require("../icons/ScatterplotIcon"));
+var _ViolinPlotIcon = _interopRequireDefault(require("../icons/ViolinPlotIcon"));
 function _interopRequireDefault(e) { return e && e.__esModule ? e : { default: e }; }
-const iconMap = {
-  [_constants.PLOT_TYPES.SCATTERPLOT]: _scatterplot.default,
-  [_constants.PLOT_TYPES.MATRIXPLOT]: _matrixplot.default,
-  [_constants.PLOT_TYPES.HEATMAP]: _heatmap.default,
-  [_constants.PLOT_TYPES.DOTPLOT]: _dotplot.default,
-  [_constants.PLOT_TYPES.VIOLINPLOT]: _violin.default
-};
-const plotTypes = Object.entries(iconMap).map(_ref => {
-  let [type, icon] = _ref;
-  return {
-    type,
-    icon,
-    alt: type.charAt(0).toUpperCase() + type.slice(1)
-  };
-});
-function PlotTypeSelector(_ref2) {
+function ownKeys(e, r) { var t = Object.keys(e); if (Object.getOwnPropertySymbols) { var o = Object.getOwnPropertySymbols(e); r && (o = o.filter(function (r) { return Object.getOwnPropertyDescriptor(e, r).enumerable; })), t.push.apply(t, o); } return t; }
+function _objectSpread(e) { for (var r = 1; r < arguments.length; r++) { var t = null != arguments[r] ? arguments[r] : {}; r % 2 ? ownKeys(Object(t), !0).forEach(function (r) { _defineProperty(e, r, t[r]); }) : Object.getOwnPropertyDescriptors ? Object.defineProperties(e, Object.getOwnPropertyDescriptors(t)) : ownKeys(Object(t)).forEach(function (r) { Object.defineProperty(e, r, Object.getOwnPropertyDescriptor(t, r)); }); } return e; }
+function _defineProperty(e, r, t) { return (r = _toPropertyKey(r)) in e ? Object.defineProperty(e, r, { value: t, enumerable: !0, configurable: !0, writable: !0 }) : e[r] = t, e; }
+function _toPropertyKey(t) { var i = _toPrimitive(t, "string"); return "symbol" == typeof i ? i : i + ""; }
+function _toPrimitive(t, r) { if ("object" != typeof t || !t) return t; var e = t[Symbol.toPrimitive]; if (void 0 !== e) { var i = e.call(t, r || "default"); if ("object" != typeof i) return i; throw new TypeError("@@toPrimitive must return a primitive value."); } return ("string" === r ? String : Number)(t); }
+const plotTypes = [{
+  type: _constants.PLOT_TYPES.SCATTERPLOT,
+  icon: _ScatterplotIcon.default,
+  name: "Scatterplot",
+  description: "Displays cells in 2D based on dimensionality reduction."
+}, {
+  type: _constants.PLOT_TYPES.MATRIXPLOT,
+  icon: _MatrixPlotIcon.default,
+  name: "Matrix Plot",
+  description: "Shows expression values of genes across categories."
+}, {
+  type: _constants.PLOT_TYPES.DOTPLOT,
+  icon: _DotPlotIcon.default,
+  name: "Dot Plot",
+  description: "Shows proportion and expression of genes across groups."
+}, {
+  type: _constants.PLOT_TYPES.HEATMAP,
+  icon: _HeatmapIcon.default,
+  name: "Heatmap",
+  description: "Visualises gene expression or feature activity as a colour-coded matrix."
+}, {
+  type: _constants.PLOT_TYPES.VIOLINPLOT,
+  icon: _ViolinPlotIcon.default,
+  name: "Violin Plot",
+  description: "Displays distribution of gene expression across categories."
+}];
+function PlotTypeSelector(_ref) {
   let {
     currentType,
     onChange
-  } = _ref2;
-  return /*#__PURE__*/_react.default.createElement("div", {
+  } = _ref;
+  const [hoveredMap, setHoveredMap] = (0, _react.useState)({});
+  const handleMouseEnter = type => setHoveredMap(prev => _objectSpread(_objectSpread({}, prev), {}, {
+    [type]: true
+  }));
+  const handleMouseLeave = type => setHoveredMap(prev => _objectSpread(_objectSpread({}, prev), {}, {
+    [type]: false
+  }));
+  return /*#__PURE__*/React.createElement("div", {
     className: "d-flex gap-2 justify-content-between"
-  }, plotTypes.map(_ref3 => {
+  }, plotTypes.map(_ref2 => {
     let {
       type,
-      icon,
-      alt
-    } = _ref3;
-    return /*#__PURE__*/_react.default.createElement("img", {
+      icon: Icon,
+      name,
+      description
+    } = _ref2;
+    const isActive = currentType === type;
+    const hovered = hoveredMap[type] || false;
+    const colour = isActive ? "#005a86" : hovered ? "#0071a7" : "#000";
+    return /*#__PURE__*/React.createElement(_StyledTooltip.StyledTooltip, {
       key: type,
-      src: icon,
-      alt: alt,
-      height: 32,
-      width: 32,
-      className: "plotselector-icon".concat(currentType === type ? " active" : ""),
+      title: /*#__PURE__*/React.createElement(React.Fragment, null, /*#__PURE__*/React.createElement("strong", null, name), /*#__PURE__*/React.createElement("br", null), description),
+      placement: "bottom",
+      slotProps: {
+        popper: {
+          modifiers: [{
+            name: "offset",
+            options: {
+              offset: [0, -12]
+            }
+          }]
+        }
+      }
+    }, /*#__PURE__*/React.createElement("div", {
+      onMouseEnter: () => handleMouseEnter(type),
+      onMouseLeave: () => handleMouseLeave(type),
       onClick: () => onChange(type),
-      style: {
-        borderBottom: currentType === type ? "2px solid #007bff" : "none"
-      },
-      title: alt
-    });
+      className: "plotselector-icon".concat(isActive ? " active" : "")
+    }, /*#__PURE__*/React.createElement(Icon, {
+      size: 34,
+      colour: colour
+    })));
   }));
 }

package/dist/cjs/components/heatmap/Heatmap.js

@@ -4,7 +4,7 @@ Object.defineProperty(exports, "__esModule", {
   value: true
 });
 exports.Heatmap = Heatmap;
-var _react = _interopRequireWildcard(require("react"));
+var _react = require("react");
 var _lodash = _interopRequireDefault(require("lodash"));
 var _reactBootstrap = require("react-bootstrap");
 var _reactPlotly = _interopRequireDefault(require("react-plotly.js"));
@@ -15,9 +15,9 @@ var _SettingsContext = require("../../context/SettingsContext");
 var _LoadingIndicators = require("../../utils/LoadingIndicators");
 var _requests = require("../../utils/requests");
 var _Resolver = require("../../utils/Resolver");
+var _PlotAlert = require("../full-page/PlotAlert");
 var _Toolbar = require("../toolbar/Toolbar");
 function _interopRequireDefault(e) { return e && e.__esModule ? e : { default: e }; }
-function _interopRequireWildcard(e, t) { if ("function" == typeof WeakMap) var r = new WeakMap(), n = new WeakMap(); return (_interopRequireWildcard = function (e, t) { if (!t && e && e.__esModule) return e; var o, i, f = { __proto__: null, default: e }; if (null === e || "object" != typeof e && "function" != typeof e) return f; if (o = t ? n : r) { if (o.has(e)) return o.get(e); o.set(e, f); } for (const t in e) "default" !== t && {}.hasOwnProperty.call(e, t) && ((i = (o = Object.defineProperty) && Object.getOwnPropertyDescriptor(e, t)) && (i.get || i.set) ? o(f, t, i) : f[t] = e[t]); return f; })(e, t); }
 function ownKeys(e, r) { var t = Object.keys(e); if (Object.getOwnPropertySymbols) { var o = Object.getOwnPropertySymbols(e); r && (o = o.filter(function (r) { return Object.getOwnPropertyDescriptor(e, r).enumerable; })), t.push.apply(t, o); } return t; }
 function _objectSpread(e) { for (var r = 1; r < arguments.length; r++) { var t = null != arguments[r] ? arguments[r] : {}; r % 2 ? ownKeys(Object(t), !0).forEach(function (r) { _defineProperty(e, r, t[r]); }) : Object.getOwnPropertyDescriptors ? Object.defineProperties(e, Object.getOwnPropertyDescriptors(t)) : ownKeys(Object(t)).forEach(function (r) { Object.defineProperty(e, r, Object.getOwnPropertyDescriptor(t, r)); }); } return e; }
 function _defineProperty(e, r, t) { return (r = _toPropertyKey(r)) in e ? Object.defineProperty(e, r, { value: t, enumerable: !0, configurable: !0, writable: !0 }) : e[r] = t, e; }
@@ -30,7 +30,9 @@ function Heatmap(_ref) {
     showCtrlsBtn = false,
     setShowObs,
     setShowVars,
-    setShowControls
+    setShowControls,
+    plotType,
+    setPlotType
   } = _ref;
   const ENDPOINT = "heatmap";
   const dataset = (0, _DatasetContext.useDataset)();
@@ -113,9 +115,9 @@ function Heatmap(_ref) {
   const modeBarButtons = customModeBarButtons.length ? [customModeBarButtons, _constants.PLOTLY_MODEBAR_BUTTONS] : [_constants.PLOTLY_MODEBAR_BUTTONS];
   if (!serverError) {
     if (hasSelections) {
-      return /*#__PURE__*/_react.default.createElement("div", {
+      return /*#__PURE__*/React.createElement("div", {
         className: "cherita-plot cherita-heatmap position-relative"
-      }, isPending && /*#__PURE__*/_react.default.createElement(_LoadingIndicators.LoadingSpinner, null), /*#__PURE__*/_react.default.createElement(_reactPlotly.default, {
+      }, isPending && /*#__PURE__*/React.createElement(_LoadingIndicators.LoadingSpinner, null), /*#__PURE__*/React.createElement(_reactPlotly.default, {
         data: data,
         layout: layout,
         useResizeHandler: true,
@@ -129,22 +131,28 @@ function Heatmap(_ref) {
         }
       }));
     }
-    return /*#__PURE__*/_react.default.createElement("div", {
-      className: "cherita-heatmap"
-    }, /*#__PURE__*/_react.default.createElement(_reactBootstrap.Alert, {
-      variant: "light"
-    }, "Select", " ", showVarsBtn ? /*#__PURE__*/_react.default.createElement(_reactBootstrap.Button, {
+    return /*#__PURE__*/React.createElement(_PlotAlert.PlotAlert, {
+      variant: "info",
+      heading: "Heatmap",
+      plotType: plotType,
+      setPlotType: setPlotType
+    }, /*#__PURE__*/React.createElement("p", {
+      className: "p-0 m-0"
+    }, "Select one or more", " ", showVarsBtn ? /*#__PURE__*/React.createElement(_reactBootstrap.Button, {
       variant: "link",
       className: "border-0 p-0 align-baseline",
       onClick: setShowVars
-    }, "features") : "features", " ", "and a", " ", showObsBtn ? /*#__PURE__*/_react.default.createElement(_reactBootstrap.Button, {
+    }, "features") : "features", " ", "to display their expression, then choose a", " ", showObsBtn ? /*#__PURE__*/React.createElement(_reactBootstrap.Button, {
       variant: "link",
       className: "border-0 p-0 align-baseline",
       onClick: setShowObs
-    }, "category") : "category"));
+    }, "category") : "category", " ", "to group observations in the heatmap."));
   } else {
-    return /*#__PURE__*/_react.default.createElement("div", null, /*#__PURE__*/_react.default.createElement(_reactBootstrap.Alert, {
-      variant: "danger"
-    }, serverError.message));
+    return /*#__PURE__*/React.createElement(_PlotAlert.PlotAlert, {
+      variant: "danger",
+      heading: "Heatmap",
+      plotType: plotType,
+      setPlotType: setPlotType
+    }, serverError.message || "An unexpected error occurred while generating the plot.");
   }
 }

package/dist/cjs/components/icons/DotPlotIcon.js

@@ -0,0 +1,58 @@
+"use strict";
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports.default = DotPlotIcon;
+const _excluded = ["size", "colour", "gap"];
+function _extends() { return _extends = Object.assign ? Object.assign.bind() : function (n) { for (var e = 1; e < arguments.length; e++) { var t = arguments[e]; for (var r in t) ({}).hasOwnProperty.call(t, r) && (n[r] = t[r]); } return n; }, _extends.apply(null, arguments); }
+function _objectWithoutProperties(e, t) { if (null == e) return {}; var o, r, i = _objectWithoutPropertiesLoose(e, t); if (Object.getOwnPropertySymbols) { var n = Object.getOwnPropertySymbols(e); for (r = 0; r < n.length; r++) o = n[r], -1 === t.indexOf(o) && {}.propertyIsEnumerable.call(e, o) && (i[o] = e[o]); } return i; }
+function _objectWithoutPropertiesLoose(r, e) { if (null == r) return {}; var t = {}; for (var n in r) if ({}.hasOwnProperty.call(r, n)) { if (-1 !== e.indexOf(n)) continue; t[n] = r[n]; } return t; }
+function DotPlotIcon(_ref) {
+  let {
+      size = 40,
+      colour = "#000",
+      gap = 20
+    } = _ref,
+    props = _objectWithoutProperties(_ref, _excluded);
+  const rows = 3;
+  const cols = 3;
+
+  // Define two radii: small and large
+  const smallR = 10;
+  const largeR = 16;
+
+  // Indices for large circles
+  const largeIndices = [1, 4, 5, 6, 7];
+
+  // Indices for semi-transparent circles
+  const semiTransparentIndices = [0, 4, 8];
+  const circles = [];
+  for (let row = 0; row < rows; row++) {
+    for (let col = 0; col < cols; col++) {
+      const index = row * cols + col;
+      const r = largeIndices.includes(index) ? largeR : smallR;
+      circles.push({
+        cx: col * (2 * largeR + gap) + largeR,
+        cy: row * (2 * largeR + gap) + largeR,
+        r,
+        fill: colour,
+        fillOpacity: semiTransparentIndices.includes(index) ? 0.5 : 1
+      });
+    }
+  }
+  const viewBoxSize = (cols - 1) * (2 * largeR + gap) + 2 * largeR;
+  return /*#__PURE__*/React.createElement("svg", _extends({
+    width: size,
+    height: size,
+    viewBox: "0 0 ".concat(viewBoxSize, " ").concat(viewBoxSize),
+    xmlns: "http://www.w3.org/2000/svg"
+  }, props), circles.map((circle, i) => /*#__PURE__*/React.createElement("circle", {
+    key: i,
+    cx: circle.cx,
+    cy: circle.cy,
+    r: circle.r,
+    fill: circle.fill,
+    fillOpacity: circle.fillOpacity
+  })));
+}

package/dist/cjs/components/icons/HeatmapIcon.js

@@ -0,0 +1,39 @@
+"use strict";
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports.default = HeatmapIcon;
+const _excluded = ["size", "colour", "gap"];
+function _extends() { return _extends = Object.assign ? Object.assign.bind() : function (n) { for (var e = 1; e < arguments.length; e++) { var t = arguments[e]; for (var r in t) ({}).hasOwnProperty.call(t, r) && (n[r] = t[r]); } return n; }, _extends.apply(null, arguments); }
+function _objectWithoutProperties(e, t) { if (null == e) return {}; var o, r, i = _objectWithoutPropertiesLoose(e, t); if (Object.getOwnPropertySymbols) { var n = Object.getOwnPropertySymbols(e); for (r = 0; r < n.length; r++) o = n[r], -1 === t.indexOf(o) && {}.propertyIsEnumerable.call(e, o) && (i[o] = e[o]); } return i; }
+function _objectWithoutPropertiesLoose(r, e) { if (null == r) return {}; var t = {}; for (var n in r) if ({}.hasOwnProperty.call(r, n)) { if (-1 !== e.indexOf(n)) continue; t[n] = r[n]; } return t; }
+function HeatmapIcon(_ref) {
+  let {
+      size = 40,
+      colour = "#000",
+      gap = 1
+    } = _ref,
+    props = _objectWithoutProperties(_ref, _excluded);
+  const rows = 6; // genes
+  const cols = 8; // cells
+
+  // Example expression pattern for visual clusters
+  const expressionLevels = [[1, 0.8, 0.2, 0.2, 0.5, 0.9, 1, 0.7], [0.9, 0.7, 0.1, 0.2, 0.4, 0.8, 0.9, 0.6], [0.1, 0.2, 0.8, 0.9, 0.7, 0.2, 0.1, 0.3], [0.2, 0.3, 0.9, 1, 0.8, 0.3, 0.2, 0.4], [0.5, 0.6, 0.2, 0.1, 0.9, 0.7, 0.6, 0.8], [0.6, 0.7, 0.3, 0.2, 0.8, 0.6, 0.7, 0.9]];
+  const cellWidth = (size - (cols - 1) * gap) / cols;
+  const cellHeight = (size - (rows - 1) * gap) / rows;
+  return /*#__PURE__*/React.createElement("svg", _extends({
+    width: size,
+    height: size,
+    viewBox: "0 0 ".concat(size, " ").concat(size),
+    xmlns: "http://www.w3.org/2000/svg"
+  }, props), expressionLevels.map((row, rowIndex) => row.map((value, colIndex) => /*#__PURE__*/React.createElement("rect", {
+    key: "".concat(rowIndex, "-").concat(colIndex),
+    x: colIndex * (cellWidth + gap),
+    y: rowIndex * (cellHeight + gap),
+    width: cellWidth,
+    height: cellHeight,
+    fill: colour,
+    fillOpacity: value
+  }))));
+}

package/dist/cjs/components/icons/MatrixPlotIcon.1.js

@@ -0,0 +1,51 @@
+"use strict";
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports.default = MatrixPlotIcon;
+const _excluded = ["size", "colour", "gap"];
+function _extends() { return _extends = Object.assign ? Object.assign.bind() : function (n) { for (var e = 1; e < arguments.length; e++) { var t = arguments[e]; for (var r in t) ({}).hasOwnProperty.call(t, r) && (n[r] = t[r]); } return n; }, _extends.apply(null, arguments); }
+function _objectWithoutProperties(e, t) { if (null == e) return {}; var o, r, i = _objectWithoutPropertiesLoose(e, t); if (Object.getOwnPropertySymbols) { var n = Object.getOwnPropertySymbols(e); for (r = 0; r < n.length; r++) o = n[r], -1 === t.indexOf(o) && {}.propertyIsEnumerable.call(e, o) && (i[o] = e[o]); } return i; }
+function _objectWithoutPropertiesLoose(r, e) { if (null == r) return {}; var t = {}; for (var n in r) if ({}.hasOwnProperty.call(r, n)) { if (-1 !== e.indexOf(n)) continue; t[n] = r[n]; } return t; }
+function MatrixPlotIcon(_ref) {
+  let {
+      size = 40,
+      colour = "#000",
+      gap = 2
+    } = _ref,
+    props = _objectWithoutProperties(_ref, _excluded);
+  const rows = 4;
+  const cols = 4;
+  const squareSize = (size - gap * (cols - 1)) / cols;
+  const squares = [];
+  for (let row = 0; row < rows; row++) {
+    for (let col = 0; col < cols; col++) {
+      squares.push({
+        x: col * (squareSize + gap),
+        y: row * (squareSize + gap)
+      });
+    }
+  }
+  const semiTransparentSquares = [0, 5, 10, 15];
+  return /*#__PURE__*/React.createElement("svg", _extends({
+    width: size,
+    height: size,
+    viewBox: "0 0 ".concat(size, " ").concat(size),
+    xmlns: "http://www.w3.org/2000/svg"
+  }, props), squares.map((_ref2, i) => {
+    let {
+      x,
+      y
+    } = _ref2;
+    return /*#__PURE__*/React.createElement("rect", {
+      key: i,
+      x: x,
+      y: y,
+      width: squareSize,
+      height: squareSize,
+      fill: colour,
+      fillOpacity: semiTransparentSquares.includes(i) ? 0.5 : 1
+    });
+  }));
+}