@haniffalab/cherita-react 1.4.1-dev.2025-10-22.61540191 → 1.4.1-dev.2025-10-23.3179e534

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Files changed (103) hide show
  1. package/dist/cjs/components/controls/Controls.js +38 -30
  2. package/dist/cjs/components/dotplot/Dotplot.js +40 -33
  3. package/dist/cjs/components/dotplot/DotplotControls.js +103 -83
  4. package/dist/cjs/components/full-page/FullPage.js +92 -69
  5. package/dist/cjs/components/full-page/PlotAlert.js +25 -16
  6. package/dist/cjs/components/full-page/PlotTypeSelector.js +43 -36
  7. package/dist/cjs/components/heatmap/Heatmap.js +40 -33
  8. package/dist/cjs/components/heatmap/HeatmapControls.js +6 -3
  9. package/dist/cjs/components/icons/DotPlotIcon.js +16 -10
  10. package/dist/cjs/components/icons/HeatmapIcon.js +17 -11
  11. package/dist/cjs/components/icons/MatrixPlotIcon.1.js +22 -16
  12. package/dist/cjs/components/icons/MatrixPlotIcon.js +22 -16
  13. package/dist/cjs/components/icons/ScatterplotIcon.1.js +21 -15
  14. package/dist/cjs/components/icons/ScatterplotIcon.js +21 -15
  15. package/dist/cjs/components/icons/ViolinPlotIcon.js +22 -14
  16. package/dist/cjs/components/matrixplot/Matrixplot.js +40 -33
  17. package/dist/cjs/components/matrixplot/MatrixplotControls.js +8 -5
  18. package/dist/cjs/components/obs-list/ObsItem.js +238 -190
  19. package/dist/cjs/components/obs-list/ObsList.js +106 -87
  20. package/dist/cjs/components/obs-list/ObsToolbar.js +2 -3
  21. package/dist/cjs/components/obsm-list/ObsmList.js +47 -32
  22. package/dist/cjs/components/offcanvas/index.js +61 -31
  23. package/dist/cjs/components/pseudospatial/Pseudospatial.js +46 -36
  24. package/dist/cjs/components/pseudospatial/PseudospatialToolbar.js +98 -68
  25. package/dist/cjs/components/scatterplot/Scatterplot.js +87 -65
  26. package/dist/cjs/components/scatterplot/ScatterplotControls.js +35 -27
  27. package/dist/cjs/components/scatterplot/SpatialControls.js +134 -107
  28. package/dist/cjs/components/scatterplot/Toolbox.js +41 -30
  29. package/dist/cjs/components/search-bar/SearchBar.js +157 -110
  30. package/dist/cjs/components/search-bar/SearchInfo.js +73 -47
  31. package/dist/cjs/components/search-bar/SearchResults.js +93 -71
  32. package/dist/cjs/components/toolbar/Toolbar.js +43 -34
  33. package/dist/cjs/components/var-list/VarItem.js +106 -79
  34. package/dist/cjs/components/var-list/VarList.js +67 -53
  35. package/dist/cjs/components/var-list/VarListToolbar.js +56 -51
  36. package/dist/cjs/components/var-list/VarSet.js +115 -97
  37. package/dist/cjs/components/violin/Violin.js +77 -58
  38. package/dist/cjs/components/violin/ViolinControls.js +8 -5
  39. package/dist/cjs/context/DatasetContext.js +20 -13
  40. package/dist/cjs/context/FilterContext.js +9 -7
  41. package/dist/cjs/context/SettingsContext.js +11 -9
  42. package/dist/cjs/context/ZarrDataContext.js +6 -5
  43. package/dist/cjs/utils/Histogram.js +35 -33
  44. package/dist/cjs/utils/ImageViewer.js +9 -6
  45. package/dist/cjs/utils/Legend.js +36 -29
  46. package/dist/cjs/utils/LoadingIndicators.js +14 -12
  47. package/dist/cjs/utils/Skeleton.js +10 -10
  48. package/dist/cjs/utils/StyledTooltip.js +7 -2
  49. package/dist/cjs/utils/VirtualizedList.js +32 -25
  50. package/dist/cjs/utils/errors.js +1 -1
  51. package/dist/css/cherita.css +6 -1
  52. package/dist/css/cherita.css.map +1 -1
  53. package/dist/esm/components/controls/Controls.js +38 -30
  54. package/dist/esm/components/dotplot/Dotplot.js +40 -33
  55. package/dist/esm/components/dotplot/DotplotControls.js +103 -82
  56. package/dist/esm/components/full-page/FullPage.js +92 -69
  57. package/dist/esm/components/full-page/PlotAlert.js +25 -16
  58. package/dist/esm/components/full-page/PlotTypeSelector.js +43 -36
  59. package/dist/esm/components/heatmap/Heatmap.js +40 -33
  60. package/dist/esm/components/heatmap/HeatmapControls.js +6 -2
  61. package/dist/esm/components/icons/DotPlotIcon.js +16 -10
  62. package/dist/esm/components/icons/HeatmapIcon.js +17 -11
  63. package/dist/esm/components/icons/MatrixPlotIcon.1.js +22 -16
  64. package/dist/esm/components/icons/MatrixPlotIcon.js +22 -16
  65. package/dist/esm/components/icons/ScatterplotIcon.1.js +21 -15
  66. package/dist/esm/components/icons/ScatterplotIcon.js +21 -15
  67. package/dist/esm/components/icons/ViolinPlotIcon.js +22 -14
  68. package/dist/esm/components/matrixplot/Matrixplot.js +40 -33
  69. package/dist/esm/components/matrixplot/MatrixplotControls.js +8 -4
  70. package/dist/esm/components/obs-list/ObsItem.js +237 -186
  71. package/dist/esm/components/obs-list/ObsList.js +106 -86
  72. package/dist/esm/components/obs-list/ObsToolbar.js +2 -2
  73. package/dist/esm/components/obsm-list/ObsmList.js +47 -31
  74. package/dist/esm/components/offcanvas/index.js +61 -31
  75. package/dist/esm/components/pseudospatial/Pseudospatial.js +46 -36
  76. package/dist/esm/components/pseudospatial/PseudospatialToolbar.js +98 -68
  77. package/dist/esm/components/scatterplot/Scatterplot.js +87 -64
  78. package/dist/esm/components/scatterplot/ScatterplotControls.js +35 -26
  79. package/dist/esm/components/scatterplot/SpatialControls.js +134 -106
  80. package/dist/esm/components/scatterplot/Toolbox.js +41 -29
  81. package/dist/esm/components/search-bar/SearchBar.js +157 -109
  82. package/dist/esm/components/search-bar/SearchInfo.js +73 -46
  83. package/dist/esm/components/search-bar/SearchResults.js +93 -70
  84. package/dist/esm/components/toolbar/Toolbar.js +43 -33
  85. package/dist/esm/components/var-list/VarItem.js +106 -78
  86. package/dist/esm/components/var-list/VarList.js +67 -52
  87. package/dist/esm/components/var-list/VarListToolbar.js +56 -50
  88. package/dist/esm/components/var-list/VarSet.js +115 -96
  89. package/dist/esm/components/violin/Violin.js +77 -58
  90. package/dist/esm/components/violin/ViolinControls.js +8 -4
  91. package/dist/esm/context/DatasetContext.js +20 -12
  92. package/dist/esm/context/FilterContext.js +9 -6
  93. package/dist/esm/context/SettingsContext.js +11 -8
  94. package/dist/esm/context/ZarrDataContext.js +6 -4
  95. package/dist/esm/utils/Histogram.js +35 -33
  96. package/dist/esm/utils/ImageViewer.js +9 -5
  97. package/dist/esm/utils/Legend.js +36 -28
  98. package/dist/esm/utils/LoadingIndicators.js +14 -11
  99. package/dist/esm/utils/Skeleton.js +10 -9
  100. package/dist/esm/utils/StyledTooltip.js +7 -2
  101. package/dist/esm/utils/VirtualizedList.js +32 -24
  102. package/dist/esm/utils/errors.js +1 -1
  103. package/package.json +3 -3
@@ -4,30 +4,34 @@ Object.defineProperty(exports, "__esModule", {
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  value: true
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  });
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  exports.ScaleSelect = exports.ColorscaleSelect = void 0;
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- var _react = _interopRequireDefault(require("react"));
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  var _lodash = _interopRequireDefault(require("lodash"));
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  var _reactBootstrap = require("react-bootstrap");
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  var _colorscales = require("../../constants/colorscales");
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  var _constants = require("../../constants/constants");
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  var _SettingsContext = require("../../context/SettingsContext");
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+ var _jsxRuntime = require("react/jsx-runtime");
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  function _interopRequireDefault(e) { return e && e.__esModule ? e : { default: e }; }
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  const ColorscaleSelect = () => {
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  const settings = (0, _SettingsContext.useSettings)();
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  const dispatch = (0, _SettingsContext.useSettingsDispatch)();
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- return /*#__PURE__*/_react.default.createElement(_reactBootstrap.Form.Group, {
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- className: "mb-2"
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- }, /*#__PURE__*/_react.default.createElement(_reactBootstrap.Form.Label, null, "Colorscale"), /*#__PURE__*/_react.default.createElement(_reactBootstrap.Form.Select, {
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- value: settings.controls.colorScale,
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- onChange: e => {
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- dispatch({
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- type: "set.controls.colorScale",
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- colorScale: e.target.value
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- });
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- }
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- }, _lodash.default.keys(_colorscales.COLORSCALES).map(key => /*#__PURE__*/_react.default.createElement("option", {
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- key: key,
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- value: key
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- }, key))));
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+ return /*#__PURE__*/(0, _jsxRuntime.jsxs)(_reactBootstrap.Form.Group, {
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+ className: "mb-2",
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+ children: [/*#__PURE__*/(0, _jsxRuntime.jsx)(_reactBootstrap.Form.Label, {
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+ children: "Colorscale"
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+ }), /*#__PURE__*/(0, _jsxRuntime.jsx)(_reactBootstrap.Form.Select, {
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+ value: settings.controls.colorScale,
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+ onChange: e => {
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+ dispatch({
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+ type: "set.controls.colorScale",
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+ colorScale: e.target.value
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+ });
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+ },
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+ children: _lodash.default.keys(_colorscales.COLORSCALES).map(key => /*#__PURE__*/(0, _jsxRuntime.jsx)("option", {
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+ value: key,
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+ children: key
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+ }, key))
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+ })]
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+ });
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  };
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  exports.ColorscaleSelect = ColorscaleSelect;
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  const ScaleSelect = _ref => {
@@ -41,20 +45,24 @@ const ScaleSelect = _ref => {
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  matrixplot: _constants.MATRIXPLOT_SCALES,
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  violinplot: _constants.VIOLINPLOT_SCALES
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  };
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- return /*#__PURE__*/_react.default.createElement(_reactBootstrap.Form.Group, {
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- className: "mb-2"
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- }, /*#__PURE__*/_react.default.createElement(_reactBootstrap.Form.Label, null, "Standard scale"), /*#__PURE__*/_react.default.createElement(_reactBootstrap.Form.Select, {
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- value: settings.controls.scale[plot] || "",
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- onChange: e => {
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- dispatch({
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- type: "set.controls.scale",
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- plot: plot,
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- scale: !e.target.value.length ? null : e.target.value
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- });
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- }
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- }, _lodash.default.values(SCALES[plot]).map(scale => /*#__PURE__*/_react.default.createElement("option", {
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- key: scale.value,
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- value: scale.value || ""
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- }, scale.name))));
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+ return /*#__PURE__*/(0, _jsxRuntime.jsxs)(_reactBootstrap.Form.Group, {
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+ className: "mb-2",
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+ children: [/*#__PURE__*/(0, _jsxRuntime.jsx)(_reactBootstrap.Form.Label, {
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+ children: "Standard scale"
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+ }), /*#__PURE__*/(0, _jsxRuntime.jsx)(_reactBootstrap.Form.Select, {
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+ value: settings.controls.scale[plot] || "",
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+ onChange: e => {
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+ dispatch({
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+ type: "set.controls.scale",
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+ plot: plot,
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+ scale: !e.target.value.length ? null : e.target.value
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+ });
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+ },
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+ children: _lodash.default.values(SCALES[plot]).map(scale => /*#__PURE__*/(0, _jsxRuntime.jsx)("option", {
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+ value: scale.value || "",
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+ children: scale.name
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+ }, scale.value))
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+ })]
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+ });
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  };
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  exports.ScaleSelect = ScaleSelect;
@@ -17,6 +17,7 @@ var _requests = require("../../utils/requests");
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  var _Resolver = require("../../utils/Resolver");
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  var _PlotAlert = require("../full-page/PlotAlert");
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  var _Toolbar = require("../toolbar/Toolbar");
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+ var _jsxRuntime = require("react/jsx-runtime");
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  function _interopRequireDefault(e) { return e && e.__esModule ? e : { default: e }; }
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  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; }
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  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; }
@@ -144,44 +145,50 @@ function Dotplot(_ref) {
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  const modeBarButtons = customModeBarButtons.length ? [customModeBarButtons, _constants.PLOTLY_MODEBAR_BUTTONS] : [_constants.PLOTLY_MODEBAR_BUTTONS];
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  if (!serverError) {
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  if (hasSelections) {
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- return /*#__PURE__*/React.createElement("div", {
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- className: "cherita-plot cherita-dotplot position-relative"
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- }, isPending && /*#__PURE__*/React.createElement(_LoadingIndicators.LoadingSpinner, null), /*#__PURE__*/React.createElement(_reactPlotly.default, {
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- data: data,
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- layout: layout,
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- useResizeHandler: true,
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- style: {
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- width: "100%",
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- height: "100%"
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- },
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- config: {
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- displaylogo: false,
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- modeBarButtons: modeBarButtons
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- }
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- }));
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+ return /*#__PURE__*/(0, _jsxRuntime.jsxs)("div", {
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+ className: "cherita-plot cherita-dotplot position-relative",
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+ children: [isPending && /*#__PURE__*/(0, _jsxRuntime.jsx)(_LoadingIndicators.LoadingSpinner, {}), /*#__PURE__*/(0, _jsxRuntime.jsx)(_reactPlotly.default, {
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+ data: data,
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+ layout: layout,
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+ useResizeHandler: true,
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+ style: {
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+ width: "100%",
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+ height: "100%"
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+ },
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+ config: {
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+ displaylogo: false,
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+ modeBarButtons: modeBarButtons
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+ }
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+ })]
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+ });
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  }
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- return /*#__PURE__*/React.createElement(_PlotAlert.PlotAlert, {
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+ return /*#__PURE__*/(0, _jsxRuntime.jsx)(_PlotAlert.PlotAlert, {
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  variant: "info",
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- heading: "Dotplot",
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+ heading: "Set up your dotplot",
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  plotType: plotType,
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- setPlotType: setPlotType
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- }, /*#__PURE__*/React.createElement("p", {
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- className: "p-0 m-0"
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- }, "Select one or more", " ", showVarsBtn ? /*#__PURE__*/React.createElement(_reactBootstrap.Button, {
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- variant: "link",
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- className: "border-0 p-0 align-baseline",
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- onClick: setShowVars
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- }, "features") : "features", " ", "to display their expression across groups, then choose a", " ", showObsBtn ? /*#__PURE__*/React.createElement(_reactBootstrap.Button, {
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- variant: "link",
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- className: "border-0 p-0 align-baseline",
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- onClick: setShowObs
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- }, "category") : "category", " ", "to group observations in the dotplot."));
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+ setPlotType: setPlotType,
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+ children: /*#__PURE__*/(0, _jsxRuntime.jsxs)("p", {
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+ className: "p-0 m-0",
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+ children: ["Select one or more", " ", showVarsBtn ? /*#__PURE__*/(0, _jsxRuntime.jsx)(_reactBootstrap.Button, {
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+ variant: "link",
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+ className: "border-0 p-0 align-baseline",
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+ onClick: setShowVars,
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+ children: "features"
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+ }) : "features", " ", "to display their expression across groups, then choose a", " ", showObsBtn ? /*#__PURE__*/(0, _jsxRuntime.jsx)(_reactBootstrap.Button, {
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+ variant: "link",
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+ className: "border-0 p-0 align-baseline",
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+ onClick: setShowObs,
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+ children: "category"
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+ }) : "category", " ", "to group observations in the dotplot."]
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+ })
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+ });
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  } else {
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- return /*#__PURE__*/React.createElement(_PlotAlert.PlotAlert, {
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+ return /*#__PURE__*/(0, _jsxRuntime.jsx)(_PlotAlert.PlotAlert, {
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  variant: "danger",
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- heading: "Dotplot",
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+ heading: "Error displaying the dotplot",
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  plotType: plotType,
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- setPlotType: setPlotType
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- }, serverError.message || "An unexpected error occurred while generating the plot.");
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+ setPlotType: setPlotType,
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+ children: serverError.message || "An unexpected error occurred while generating the plot."
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+ });
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  }
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  }
@@ -4,11 +4,11 @@ Object.defineProperty(exports, "__esModule", {
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  value: true
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  });
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  exports.DotplotControls = DotplotControls;
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- var _react = _interopRequireWildcard(require("react"));
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+ var _react = require("react");
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  var _reactBootstrap = require("react-bootstrap");
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  var _SettingsContext = require("../../context/SettingsContext");
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  var _Controls = require("../controls/Controls");
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- 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); }
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+ var _jsxRuntime = require("react/jsx-runtime");
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  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; }
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  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; }
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@@ -33,88 +33,108 @@ function DotplotControls() {
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  expressionCutoff: settings.controls.expressionCutoff
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  }));
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  }, [settings.controls.colorAxis.cmin, settings.controls.colorAxis.cmax, settings.controls.expressionCutoff]);
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- return /*#__PURE__*/_react.default.createElement(_react.default.Fragment, null, /*#__PURE__*/_react.default.createElement(_reactBootstrap.Form, null, /*#__PURE__*/_react.default.createElement(_Controls.ColorscaleSelect, null), /*#__PURE__*/_react.default.createElement(_reactBootstrap.Form.Group, {
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- className: "mb-2"
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- }, /*#__PURE__*/_react.default.createElement(_reactBootstrap.InputGroup, null, /*#__PURE__*/_react.default.createElement(_reactBootstrap.InputGroup.Text, null, "min"), /*#__PURE__*/_react.default.createElement(_reactBootstrap.Form.Control, {
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- name: "scaleMin",
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- size: "sm",
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- type: "number",
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- value: controls.colorAxis.cmin,
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- step: 0.1,
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- min: Math.min(settings.controls.colorAxis.dmin, 0.0),
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- max: settings.controls.colorAxis.dmax,
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- onChange: e => {
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- setControls(_objectSpread(_objectSpread({}, controls), {}, {
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- colorAxis: _objectSpread(_objectSpread({}, controls.colorAxis), {}, {
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- cmin: e.target.value
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+ return /*#__PURE__*/(0, _jsxRuntime.jsx)(_jsxRuntime.Fragment, {
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+ children: /*#__PURE__*/(0, _jsxRuntime.jsxs)(_reactBootstrap.Form, {
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+ children: [/*#__PURE__*/(0, _jsxRuntime.jsx)(_Controls.ColorscaleSelect, {}), /*#__PURE__*/(0, _jsxRuntime.jsx)(_reactBootstrap.Form.Group, {
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+ className: "mb-2",
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+ children: /*#__PURE__*/(0, _jsxRuntime.jsxs)(_reactBootstrap.InputGroup, {
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+ children: [/*#__PURE__*/(0, _jsxRuntime.jsx)(_reactBootstrap.InputGroup.Text, {
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+ children: "min"
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+ }), /*#__PURE__*/(0, _jsxRuntime.jsx)(_reactBootstrap.Form.Control, {
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+ name: "scaleMin",
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+ size: "sm",
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+ type: "number",
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+ value: controls.colorAxis.cmin,
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+ step: 0.1,
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+ min: Math.min(settings.controls.colorAxis.dmin, 0.0),
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+ max: settings.controls.colorAxis.dmax,
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+ onChange: e => {
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+ setControls(_objectSpread(_objectSpread({}, controls), {}, {
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+ colorAxis: _objectSpread(_objectSpread({}, controls.colorAxis), {}, {
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+ cmin: e.target.value
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+ })
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+ }));
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+ }
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+ }), /*#__PURE__*/(0, _jsxRuntime.jsx)(_reactBootstrap.InputGroup.Text, {
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+ children: "max"
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+ }), /*#__PURE__*/(0, _jsxRuntime.jsx)(_reactBootstrap.Form.Control, {
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+ name: "scaleMax",
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+ size: "sm",
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+ type: "number",
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+ value: controls.colorAxis.cmax,
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+ step: 0.1,
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+ min: controls.colorAxis.cmin,
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+ max: settings.controls.colorAxis.dmax,
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+ onChange: e => {
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+ if (parseFloat(e.target.value) > settings.controls.colorAxis.dmax) {
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+ e.target.value = settings.controls.colorAxis.dmax.toFixed(1);
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  }
@@ -7,11 +7,11 @@ exports.FullPage = FullPage;
7
7
  var _react = require("react");
8
8
  var _material = require("@mui/material");
9
9
  var _reactBootstrap = require("react-bootstrap");
10
+ var _PlotTypeSelector = require("./PlotTypeSelector");
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11
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11
12
  var _DatasetContext = require("../../context/DatasetContext");
12
13
  var _Dotplot = require("../dotplot/Dotplot");
13
14
  var _DotplotControls = require("../dotplot/DotplotControls");
14
- var _PlotTypeSelector = require("../full-page/PlotTypeSelector");
15
15
  var _Heatmap = require("../heatmap/Heatmap");
16
16
  var _HeatmapControls = require("../heatmap/HeatmapControls");
17
17
  var _Matrixplot = require("../matrixplot/Matrixplot");
@@ -26,8 +26,13 @@ var _SearchBar = require("../search-bar/SearchBar");
26
26
  var _VarList = require("../var-list/VarList");
27
27
  var _Violin = require("../violin/Violin");
28
28
  var _ViolinControls = require("../violin/ViolinControls");
29
+ var _jsxRuntime = require("react/jsx-runtime");
29
30
  const _excluded = ["searchDiseases", "defaultPlotType"];
30
- 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); }
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33
38
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@@ -99,82 +104,100 @@ function FullPage(_ref) {
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104
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106
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- return /*#__PURE__*/React.createElement(_Matrixplot.Matrixplot, commonProps);
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+ return /*#__PURE__*/(0, _jsxRuntime.jsx)(_Matrixplot.Matrixplot, _objectSpread({}, commonProps));
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- return /*#__PURE__*/React.createElement(_Heatmap.Heatmap, commonProps);
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112
117
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180
203
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