@haniffalab/cherita-react 1.4.1 → 1.4.2-dev.2025-10-29.81a6b906

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (138) hide show
  1. package/README.md +1 -1
  2. package/dist/cjs/components/controls/Controls.js +38 -30
  3. package/dist/cjs/components/dotplot/Dotplot.js +67 -69
  4. package/dist/cjs/components/dotplot/DotplotControls.js +103 -83
  5. package/dist/cjs/components/full-page/FullPage.js +100 -74
  6. package/dist/cjs/components/full-page/PlotAlert.js +45 -0
  7. package/dist/cjs/components/full-page/PlotTypeSelector.js +89 -44
  8. package/dist/cjs/components/heatmap/Heatmap.js +65 -65
  9. package/dist/cjs/components/heatmap/HeatmapControls.js +6 -3
  10. package/dist/cjs/components/icons/DotPlotIcon.js +64 -0
  11. package/dist/cjs/components/icons/HeatmapIcon.js +45 -0
  12. package/dist/cjs/components/icons/MatrixPlotIcon.1.js +57 -0
  13. package/dist/cjs/components/icons/MatrixPlotIcon.js +59 -0
  14. package/dist/cjs/components/icons/ScatterplotIcon.1.js +164 -0
  15. package/dist/cjs/components/icons/ScatterplotIcon.js +144 -0
  16. package/dist/cjs/components/icons/ViolinPlotIcon.js +42 -0
  17. package/dist/cjs/components/matrixplot/Matrixplot.js +65 -66
  18. package/dist/cjs/components/matrixplot/MatrixplotControls.js +8 -5
  19. package/dist/cjs/components/obs-list/ObsItem.js +258 -210
  20. package/dist/cjs/components/obs-list/ObsList.js +161 -133
  21. package/dist/cjs/components/obs-list/ObsToolbar.js +2 -3
  22. package/dist/cjs/components/obsm-list/ObsmList.js +53 -38
  23. package/dist/cjs/components/offcanvas/index.js +61 -31
  24. package/dist/cjs/components/pseudospatial/Pseudospatial.js +132 -76
  25. package/dist/cjs/components/pseudospatial/PseudospatialToolbar.js +122 -74
  26. package/dist/cjs/components/scatterplot/Scatterplot.js +127 -99
  27. package/dist/cjs/components/scatterplot/ScatterplotControls.js +45 -31
  28. package/dist/cjs/components/scatterplot/SpatialControls.js +140 -113
  29. package/dist/cjs/components/scatterplot/Toolbox.js +41 -30
  30. package/dist/cjs/components/search-bar/SearchBar.js +168 -121
  31. package/dist/cjs/components/search-bar/SearchInfo.js +76 -50
  32. package/dist/cjs/components/search-bar/SearchResults.js +93 -71
  33. package/dist/cjs/components/toolbar/Toolbar.js +46 -37
  34. package/dist/cjs/components/var-list/VarItem.js +115 -88
  35. package/dist/cjs/components/var-list/VarList.js +85 -69
  36. package/dist/cjs/components/var-list/VarListToolbar.js +59 -54
  37. package/dist/cjs/components/var-list/VarSet.js +126 -108
  38. package/dist/cjs/components/violin/Violin.js +109 -107
  39. package/dist/cjs/components/violin/ViolinControls.js +8 -5
  40. package/dist/cjs/constants/colorscales.js +19 -19
  41. package/dist/cjs/constants/constants.js +47 -47
  42. package/dist/cjs/context/DatasetContext.js +24 -16
  43. package/dist/cjs/context/FilterContext.js +11 -9
  44. package/dist/cjs/context/SettingsContext.js +255 -89
  45. package/dist/cjs/context/ZarrDataContext.js +6 -5
  46. package/dist/cjs/helpers/color-helper.js +2 -2
  47. package/dist/cjs/helpers/zarr-helper.js +3 -3
  48. package/dist/cjs/utils/Filter.js +16 -11
  49. package/dist/cjs/utils/Histogram.js +35 -33
  50. package/dist/cjs/utils/ImageViewer.js +11 -8
  51. package/dist/cjs/utils/Legend.js +37 -30
  52. package/dist/cjs/utils/LoadingIndicators.js +15 -13
  53. package/dist/cjs/utils/Resolver.js +213 -0
  54. package/dist/cjs/utils/Skeleton.js +10 -10
  55. package/dist/cjs/utils/StyledTooltip.js +44 -0
  56. package/dist/cjs/utils/VirtualizedList.js +34 -27
  57. package/dist/cjs/utils/errors.js +15 -15
  58. package/dist/cjs/utils/requests.js +21 -9
  59. package/dist/cjs/utils/search.js +4 -4
  60. package/dist/cjs/utils/string.js +6 -6
  61. package/dist/cjs/utils/zarrData.js +20 -21
  62. package/dist/css/cherita.css +64 -42
  63. package/dist/css/cherita.css.map +1 -1
  64. package/dist/esm/components/controls/Controls.js +43 -35
  65. package/dist/esm/components/dotplot/Dotplot.js +77 -78
  66. package/dist/esm/components/dotplot/DotplotControls.js +106 -85
  67. package/dist/esm/components/full-page/FullPage.js +120 -93
  68. package/dist/esm/components/full-page/PlotAlert.js +39 -0
  69. package/dist/esm/components/full-page/PlotTypeSelector.js +90 -45
  70. package/dist/esm/components/heatmap/Heatmap.js +75 -74
  71. package/dist/esm/components/heatmap/HeatmapControls.js +8 -4
  72. package/dist/esm/components/icons/DotPlotIcon.js +58 -0
  73. package/dist/esm/components/icons/HeatmapIcon.js +39 -0
  74. package/dist/esm/components/icons/MatrixPlotIcon.1.js +51 -0
  75. package/dist/esm/components/icons/MatrixPlotIcon.js +53 -0
  76. package/dist/esm/components/icons/ScatterplotIcon.1.js +158 -0
  77. package/dist/esm/components/icons/ScatterplotIcon.js +138 -0
  78. package/dist/esm/components/icons/ViolinPlotIcon.js +36 -0
  79. package/dist/esm/components/matrixplot/Matrixplot.js +75 -75
  80. package/dist/esm/components/matrixplot/MatrixplotControls.js +10 -6
  81. package/dist/esm/components/obs-list/ObsItem.js +273 -222
  82. package/dist/esm/components/obs-list/ObsList.js +176 -147
  83. package/dist/esm/components/obs-list/ObsToolbar.js +3 -3
  84. package/dist/esm/components/obsm-list/ObsmList.js +60 -44
  85. package/dist/esm/components/offcanvas/index.js +67 -37
  86. package/dist/esm/components/pseudospatial/Pseudospatial.js +145 -88
  87. package/dist/esm/components/pseudospatial/PseudospatialToolbar.js +127 -78
  88. package/dist/esm/components/scatterplot/Scatterplot.js +148 -119
  89. package/dist/esm/components/scatterplot/ScatterplotControls.js +50 -35
  90. package/dist/esm/components/scatterplot/SpatialControls.js +153 -125
  91. package/dist/esm/components/scatterplot/Toolbox.js +44 -32
  92. package/dist/esm/components/search-bar/SearchBar.js +180 -132
  93. package/dist/esm/components/search-bar/SearchInfo.js +86 -59
  94. package/dist/esm/components/search-bar/SearchResults.js +100 -77
  95. package/dist/esm/components/toolbar/Toolbar.js +49 -39
  96. package/dist/esm/components/var-list/VarItem.js +126 -98
  97. package/dist/esm/components/var-list/VarList.js +99 -82
  98. package/dist/esm/components/var-list/VarListToolbar.js +64 -58
  99. package/dist/esm/components/var-list/VarSet.js +134 -115
  100. package/dist/esm/components/violin/Violin.js +121 -118
  101. package/dist/esm/components/violin/ViolinControls.js +10 -6
  102. package/dist/esm/constants/colorscales.js +19 -19
  103. package/dist/esm/constants/constants.js +47 -47
  104. package/dist/esm/context/DatasetContext.js +31 -22
  105. package/dist/esm/context/FilterContext.js +11 -8
  106. package/dist/esm/context/SettingsContext.js +257 -90
  107. package/dist/esm/context/ZarrDataContext.js +8 -6
  108. package/dist/esm/helpers/color-helper.js +5 -5
  109. package/dist/esm/helpers/map-helper.js +2 -2
  110. package/dist/esm/helpers/zarr-helper.js +6 -6
  111. package/dist/esm/index.js +22 -22
  112. package/dist/esm/utils/Filter.js +22 -17
  113. package/dist/esm/utils/Histogram.js +39 -37
  114. package/dist/esm/utils/ImageViewer.js +12 -8
  115. package/dist/esm/utils/Legend.js +44 -36
  116. package/dist/esm/utils/LoadingIndicators.js +16 -13
  117. package/dist/esm/utils/Resolver.js +201 -0
  118. package/dist/esm/utils/Skeleton.js +11 -10
  119. package/dist/esm/utils/StyledTooltip.js +38 -0
  120. package/dist/esm/utils/VirtualizedList.js +35 -27
  121. package/dist/esm/utils/errors.js +15 -15
  122. package/dist/esm/utils/requests.js +24 -12
  123. package/dist/esm/utils/search.js +7 -7
  124. package/dist/esm/utils/string.js +7 -7
  125. package/dist/esm/utils/zarrData.js +27 -28
  126. package/package.json +21 -9
  127. package/scss/cherita-bootstrap.scss +2 -2
  128. package/scss/cherita.scss +43 -17
  129. package/scss/components/accordions.scss +4 -1
  130. package/scss/components/layouts.scss +15 -33
  131. package/scss/components/lists.scss +8 -4
  132. package/scss/components/plotly.scss +38 -26
  133. package/scss/components/plots.scss +14 -1
  134. package/dist/assets/images/plots/dotplot.svg +0 -152
  135. package/dist/assets/images/plots/heatmap.svg +0 -193
  136. package/dist/assets/images/plots/matrixplot.svg +0 -275
  137. package/dist/assets/images/plots/scatterplot.svg +0 -198
  138. package/dist/assets/images/plots/violin.svg +0 -50
@@ -1,26 +1,30 @@
1
- import React from "react";
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- import _ from "lodash";
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- import { Form } from "react-bootstrap";
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- import { COLORSCALES } from "../../constants/colorscales";
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- import { DOTPLOT_SCALES, MATRIXPLOT_SCALES, VIOLINPLOT_SCALES } from "../../constants/constants";
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- import { useSettings, useSettingsDispatch } from "../../context/SettingsContext";
1
+ import _ from 'lodash';
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+ import { Form } from 'react-bootstrap';
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+ import { COLORSCALES } from '../../constants/colorscales';
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+ import { DOTPLOT_SCALES, MATRIXPLOT_SCALES, VIOLINPLOT_SCALES } from '../../constants/constants';
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+ import { useSettings, useSettingsDispatch } from '../../context/SettingsContext';
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+ import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
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  export const ColorscaleSelect = () => {
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  const settings = useSettings();
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  const dispatch = useSettingsDispatch();
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- return /*#__PURE__*/React.createElement(Form.Group, {
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- className: "mb-2"
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- }, /*#__PURE__*/React.createElement(Form.Label, null, "Colorscale"), /*#__PURE__*/React.createElement(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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- }, _.keys(COLORSCALES).map(key => /*#__PURE__*/React.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__*/_jsxs(Form.Group, {
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+ className: "mb-2",
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+ children: [/*#__PURE__*/_jsx(Form.Label, {
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+ children: "Colorscale"
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+ }), /*#__PURE__*/_jsx(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: _.keys(COLORSCALES).map(key => /*#__PURE__*/_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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+ });
24
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  };
25
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  export const ScaleSelect = _ref => {
26
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  let {
@@ -33,19 +37,23 @@ export const ScaleSelect = _ref => {
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  matrixplot: MATRIXPLOT_SCALES,
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  violinplot: VIOLINPLOT_SCALES
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  };
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- return /*#__PURE__*/React.createElement(Form.Group, {
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- className: "mb-2"
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- }, /*#__PURE__*/React.createElement(Form.Label, null, "Standard scale"), /*#__PURE__*/React.createElement(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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- }, _.values(SCALES[plot]).map(scale => /*#__PURE__*/React.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__*/_jsxs(Form.Group, {
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+ className: "mb-2",
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+ children: [/*#__PURE__*/_jsx(Form.Label, {
43
+ children: "Standard scale"
44
+ }), /*#__PURE__*/_jsx(Form.Select, {
45
+ value: settings.controls.scale[plot] || '',
46
+ onChange: e => {
47
+ dispatch({
48
+ type: 'set.controls.scale',
49
+ plot: plot,
50
+ scale: !e.target.value.length ? null : e.target.value
51
+ });
52
+ },
53
+ children: _.values(SCALES[plot]).map(scale => /*#__PURE__*/_jsx("option", {
54
+ value: scale.value || '',
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+ children: scale.name
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+ }, scale.value))
57
+ })]
58
+ });
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  };
@@ -3,28 +3,32 @@ function _objectSpread(e) { for (var r = 1; r < arguments.length; r++) { var t =
3
3
  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; }
4
4
  function _toPropertyKey(t) { var i = _toPrimitive(t, "string"); return "symbol" == typeof i ? i : i + ""; }
5
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  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); }
6
- import React, { useCallback, useEffect, useRef, useState } from "react";
7
- import _ from "lodash";
8
- import { Alert, Button } from "react-bootstrap";
9
- import Plot from "react-plotly.js";
10
- import { PLOTLY_MODEBAR_BUTTONS } from "../../constants/constants";
11
- import { useDataset } from "../../context/DatasetContext";
12
- import { useFilteredData } from "../../context/FilterContext";
13
- import { useSettings, useSettingsDispatch } from "../../context/SettingsContext";
14
- import { LoadingSpinner } from "../../utils/LoadingIndicators";
15
- import { useDebouncedFetch } from "../../utils/requests";
16
- import { ControlsPlotlyToolbar, ObsPlotlyToolbar, VarPlotlyToolbar } from "../toolbar/Toolbar";
6
+ import { useCallback, useEffect, useMemo, useRef, useState } from 'react';
7
+ import _ from 'lodash';
8
+ import { Button } from 'react-bootstrap';
9
+ import Plot from 'react-plotly.js';
10
+ import { PLOTLY_MODEBAR_BUTTONS } from '../../constants/constants';
11
+ import { useDataset } from '../../context/DatasetContext';
12
+ import { useFilteredData } from '../../context/FilterContext';
13
+ import { useSettings, useSettingsDispatch } from '../../context/SettingsContext';
14
+ import { LoadingSpinner } from '../../utils/LoadingIndicators';
15
+ import { useDebouncedFetch } from '../../utils/requests';
16
+ import { useSelectedMultiVar, useSelectedObs } from '../../utils/Resolver';
17
+ import { PlotAlert } from '../full-page/PlotAlert';
18
+ import { ControlsPlotlyToolbar, ObsPlotlyToolbar, VarPlotlyToolbar } from '../toolbar/Toolbar';
19
+ import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
17
20
  export function Dotplot(_ref) {
18
- var _settings$selectedObs, _settings$selectedObs2, _settings$selectedObs3;
19
21
  let {
20
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  showObsBtn = false,
21
23
  showVarsBtn = false,
22
24
  showCtrlsBtn = false,
23
25
  setShowObs,
24
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  setShowVars,
25
- setShowControls
27
+ setShowControls,
28
+ plotType,
29
+ setPlotType
26
30
  } = _ref;
27
- const ENDPOINT = "dotplot";
31
+ const ENDPOINT = 'dotplot';
28
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  const dataset = useDataset();
29
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  const settings = useSettings();
30
34
  const {
@@ -36,14 +40,13 @@ export function Dotplot(_ref) {
36
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  const [data, setData] = useState([]);
37
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  const [layout, setLayout] = useState({});
38
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  const [hasSelections, setHasSelections] = useState(false);
39
- const [params, setParams] = useState({
43
+ const selectedObs = useSelectedObs();
44
+ const selectedMultiVar = useSelectedMultiVar();
45
+ const params = useMemo(() => ({
40
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  url: dataset.url,
41
- obsCol: settings.selectedObs,
42
- obsValues: !((_settings$selectedObs = settings.selectedObs) !== null && _settings$selectedObs !== void 0 && _settings$selectedObs.omit.length) ? null : _.difference(_.values((_settings$selectedObs2 = settings.selectedObs) === null || _settings$selectedObs2 === void 0 ? void 0 : _settings$selectedObs2.codes), (_settings$selectedObs3 = settings.selectedObs) === null || _settings$selectedObs3 === void 0 ? void 0 : _settings$selectedObs3.omit).map(c => {
43
- var _settings$selectedObs4;
44
- return (_settings$selectedObs4 = settings.selectedObs) === null || _settings$selectedObs4 === void 0 ? void 0 : _settings$selectedObs4.codesMap[c];
45
- }),
46
- varKeys: settings.selectedMultiVar.map(i => i.isSet ? {
47
+ obsCol: selectedObs,
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+ obsValues: !(selectedObs !== null && selectedObs !== void 0 && selectedObs.omit.length) ? null : _.difference(selectedObs === null || selectedObs === void 0 ? void 0 : selectedObs.values, selectedObs === null || selectedObs === void 0 ? void 0 : selectedObs.omit),
49
+ varKeys: selectedMultiVar.map(i => i.isSet ? {
47
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  name: i.name,
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  indices: i.vars.map(v => v.index)
49
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  } : i.index),
@@ -52,36 +55,16 @@ export function Dotplot(_ref) {
52
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  meanOnlyExpressed: settings.controls.meanOnlyExpressed,
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  expressionCutoff: settings.controls.expressionCutoff,
54
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  varNamesCol: dataset.varNamesCol
55
- });
58
+ }), [dataset.url, dataset.varNamesCol, isSliced, obsIndices, selectedMultiVar, selectedObs, settings.controls.expressionCutoff, settings.controls.meanOnlyExpressed, settings.controls.scale.dotplot]);
56
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  // @TODO: set default scale
57
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58
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  useEffect(() => {
59
- if (settings.selectedObs && settings.selectedMultiVar.length) {
62
+ if (selectedObs && selectedMultiVar.length) {
60
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  setHasSelections(true);
61
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  } else {
62
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  setHasSelections(false);
63
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  }
64
- setParams(p => {
65
- var _settings$selectedObs5, _settings$selectedObs6, _settings$selectedObs7;
66
- return _objectSpread(_objectSpread({}, p), {}, {
67
- url: dataset.url,
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- obsCol: settings.selectedObs,
69
- obsValues: !((_settings$selectedObs5 = settings.selectedObs) !== null && _settings$selectedObs5 !== void 0 && _settings$selectedObs5.omit.length) ? null : _.difference(_.values((_settings$selectedObs6 = settings.selectedObs) === null || _settings$selectedObs6 === void 0 ? void 0 : _settings$selectedObs6.codes), (_settings$selectedObs7 = settings.selectedObs) === null || _settings$selectedObs7 === void 0 ? void 0 : _settings$selectedObs7.omit).map(c => {
70
- var _settings$selectedObs8;
71
- return (_settings$selectedObs8 = settings.selectedObs) === null || _settings$selectedObs8 === void 0 ? void 0 : _settings$selectedObs8.codesMap[c];
72
- }),
73
- varKeys: settings.selectedMultiVar.map(i => i.isSet ? {
74
- name: i.name,
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- indices: i.vars.map(v => v.index)
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- } : i.index),
77
- obsIndices: isSliced ? [...(obsIndices || [])] : null,
78
- standardScale: settings.controls.scale.dotplot,
79
- meanOnlyExpressed: settings.controls.meanOnlyExpressed,
80
- expressionCutoff: settings.controls.expressionCutoff,
81
- varNamesCol: dataset.varNamesCol
82
- });
83
- });
84
- }, [dataset.url, settings.selectedObs, settings.selectedMultiVar, settings.controls.scale.dotplot, settings.controls.meanOnlyExpressed, settings.controls.expressionCutoff, dataset.varNamesCol, isSliced, obsIndices]);
67
+ }, [dataset.url, selectedObs, settings.controls.scale.dotplot, settings.controls.meanOnlyExpressed, settings.controls.expressionCutoff, dataset.varNamesCol, isSliced, obsIndices, selectedMultiVar]);
85
68
  const updateColorscale = useCallback(colorscale => {
86
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  setLayout(l => {
87
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  return _objectSpread(_objectSpread({}, l), {}, {
@@ -96,14 +79,15 @@ export function Dotplot(_ref) {
96
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  isPending,
97
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  serverError
98
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  } = useDebouncedFetch(ENDPOINT, params, 500, {
99
- enabled: !!params.obsCol && !!params.varKeys.length
82
+ isEnabled: params => !!params.obsCol && !!params.varKeys.length
100
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  });
101
84
  useEffect(() => {
102
- if (hasSelections && !isPending && !serverError) {
85
+ if (hasSelections && !!fetchedData && !isPending && !serverError) {
103
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  setData(fetchedData.data);
104
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  setLayout(fetchedData.layout);
88
+ // @TODO: keep colorAxis range from settings
105
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  dispatch({
106
- type: "set.controls.colorAxis",
90
+ type: 'set.controls.colorAxis',
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  colorAxis: {
108
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  dmin: fetchedData.range.min.toFixed(1),
109
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  dmax: fetchedData.range.max.toFixed(1),
@@ -112,6 +96,9 @@ export function Dotplot(_ref) {
112
96
  }
113
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  });
114
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  updateColorscale(colorscale.current);
99
+ } else {
100
+ setData([]);
101
+ setLayout({});
115
102
  }
116
103
  }, [fetchedData, isPending, serverError, hasSelections, dispatch, updateColorscale]);
117
104
  useEffect(() => {
@@ -138,38 +125,50 @@ export function Dotplot(_ref) {
138
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  const modeBarButtons = customModeBarButtons.length ? [customModeBarButtons, PLOTLY_MODEBAR_BUTTONS] : [PLOTLY_MODEBAR_BUTTONS];
139
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  if (!serverError) {
140
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  if (hasSelections) {
141
- return /*#__PURE__*/React.createElement("div", {
142
- className: "cherita-plot cherita-dotplot position-relative"
143
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+ }
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+ children: /*#__PURE__*/_jsxs("p", {
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+ className: "border-0 p-0 align-baseline",
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+ }) : 'features', ' ', "to display their expression across groups, then choose a", ' ', showObsBtn ? /*#__PURE__*/_jsx(Button, {
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+ className: "border-0 p-0 align-baseline",
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@@ -3,10 +3,11 @@ function _objectSpread(e) { for (var r = 1; r < arguments.length; r++) { var t =
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- import { useSettings, useSettingsDispatch } from "../../context/SettingsContext";
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- import { ColorscaleSelect, ScaleSelect } from "../controls/Controls";
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+ import { useEffect, useState } from 'react';
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+ import { Button, Form, InputGroup } from 'react-bootstrap';
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+ import { useSettings, useSettingsDispatch } from '../../context/SettingsContext';
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+ import { ColorscaleSelect, ScaleSelect } from '../controls/Controls';
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+ import { jsx as _jsx, jsxs as _jsxs, Fragment as _Fragment } from "react/jsx-runtime";
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11
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  const settings = useSettings();
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  const dispatch = useSettingsDispatch();
@@ -26,88 +27,108 @@ export function DotplotControls() {
26
27
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- setControls(_objectSpread(_objectSpread({}, controls), {}, {
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+ onChange: e => {
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