@vitessce/statistical-plots 4.0.0 → 4.0.2

package/dist/{deflate-DW1iET8g.js → deflate-DN9irvtS.js}

@@ -1,5 +1,5 @@
 import { i as inflate_1 } from "./pako.esm-SxljTded.js";
-import { B as BaseDecoder } from "./index-DKGZofDL.js";
+import { B as BaseDecoder } from "./index-DKWiD0_-.js";
 class DeflateDecoder extends BaseDecoder {
   decodeBlock(buffer) {
     return inflate_1(new Uint8Array(buffer)).buffer;

package/dist/{index-DKGZofDL.js → index-DKWiD0_-.js}

@@ -357,6 +357,7 @@ const CoordinationType$1 = {
   SPATIAL_CHANNEL_LABELS_VISIBLE: "spatialChannelLabelsVisible",
   SPATIAL_CHANNEL_LABELS_ORIENTATION: "spatialChannelLabelsOrientation",
   SPATIAL_CHANNEL_LABEL_SIZE: "spatialChannelLabelSize",
+  SPATIAL_CHANNELS_SORT_ORDER: "spatialChannelsSortOrder",
   // Multi-sample / comparative
   SAMPLE_TYPE: "sampleType",
   SAMPLE_SELECTION: "sampleSelection",
@@ -942,6 +943,7 @@ const COMPONENT_COORDINATION_TYPES = {
     CoordinationType$1.SPATIAL_CHANNEL_LABELS_VISIBLE,
     CoordinationType$1.SPATIAL_CHANNEL_LABELS_ORIENTATION,
     CoordinationType$1.SPATIAL_CHANNEL_LABEL_SIZE,
+    CoordinationType$1.SPATIAL_CHANNELS_SORT_ORDER,
     CoordinationType$1.PHOTOMETRIC_INTERPRETATION
   ],
   [ViewType$1.HEATMAP]: [
@@ -1123,7 +1125,8 @@ const COMPONENT_COORDINATION_TYPES = {
     CoordinationType$1.LEGEND_VISIBLE,
     CoordinationType$1.SPATIAL_CHANNEL_LABELS_VISIBLE,
     CoordinationType$1.SPATIAL_CHANNEL_LABELS_ORIENTATION,
-    CoordinationType$1.SPATIAL_CHANNEL_LABEL_SIZE
+    CoordinationType$1.SPATIAL_CHANNEL_LABEL_SIZE,
+    CoordinationType$1.SPATIAL_CHANNELS_SORT_ORDER
   ],
   [ViewType$1.GENOMIC_PROFILES]: [
     CoordinationType$1.DATASET,
@@ -11591,7 +11594,18 @@ z.object({
 z.object({
   projectionAnnotationSpacing: z.number(),
   featureIndexProp: z.string().optional().describe("The name of the Neuroglancer AnnotationProperty containing feature IDs. For example, specify 'gene' to use prop_gene() in the Neuroglancer shader code."),
-  pointIndexProp: z.string().optional().describe("The name of the Neuroglancer AnnotationProperty containing point IDs. For example, specify 'point_id' to use prop_point_id() in the Neuroglancer shader code.")
+  pointIndexProp: z.string().optional().describe("The name of the Neuroglancer AnnotationProperty containing point IDs. For example, specify 'point_id' to use prop_point_id() in the Neuroglancer shader code."),
+  transform: z.object({
+    matrix: z.array(z.array(z.number())),
+    outputDimensions: z.record(z.tuple([z.number(), z.string()]))
+  }).optional().describe("A coordinate transformation matrix to apply to the annotation layer source to map annotation coordinates to the global coordinate space."),
+  // Note: See comments in neuroglancer-sorger.js
+  // We may remove these in the future, pending clarification
+  // to questions in the tissue-map-tools repo
+  // - https://github.com/hms-dbmi/tissue-map-tools/issues/20
+  // - https://github.com/hms-dbmi/tissue-map-tools/issues/38
+  quantitativeColorProp: z.string().optional(),
+  quantitativeColorMax: z.number().optional()
 }).partial().nullable();
 z.object({
   obsIndex: z.string(),
@@ -18166,6 +18180,37 @@ function keyof(value2) {
   return value2 !== null && typeof value2 === "object" ? value2.valueOf() : value2;
 }
 const schemeRdBu = [[103, 0, 31], [178, 24, 43], [214, 96, 77], [244, 165, 130], [253, 219, 199], [247, 247, 247], [209, 229, 240], [146, 197, 222], [67, 147, 195], [33, 102, 172], [5, 48, 97]];
+const schemePlasma = [[13, 8, 135], [16, 7, 136], [19, 7, 137], [22, 7, 138], [25, 6, 140], [27, 6, 141], [29, 6, 142], [32, 6, 143], [34, 6, 144], [36, 6, 145], [38, 5, 145], [40, 5, 146], [42, 5, 147], [44, 5, 148], [46, 5, 149], [47, 5, 150], [49, 5, 151], [51, 5, 151], [53, 4, 152], [55, 4, 153], [56, 4, 154], [58, 4, 154], [60, 4, 155], [62, 4, 156], [63, 4, 156], [65, 4, 157], [67, 3, 158], [68, 3, 158], [70, 3, 159], [72, 3, 159], [73, 3, 160], [75, 3, 161], [76, 2, 161], [78, 2, 162], [80, 2, 162], [81, 2, 163], [83, 2, 163], [85, 2, 164], [86, 1, 164], [88, 1, 164], [89, 1, 165], [91, 1, 165], [92, 1, 166], [94, 1, 166], [96, 1, 166], [97, 0, 167], [99, 0, 167], [100, 0, 167], [102, 0, 167], [103, 0, 168], [105, 0, 168], [106, 0, 168], [108, 0, 168], [110, 0, 168], [111, 0, 168], [113, 0, 168], [114, 1, 168], [116, 1, 168], [117, 1, 168], [119, 1, 168], [120, 1, 168], [122, 2, 168], [123, 2, 168], [125, 3, 168], [126, 3, 168], [128, 4, 168], [129, 4, 167], [131, 5, 167], [132, 5, 167], [134, 6, 166], [135, 7, 166], [136, 8, 166], [138, 9, 165], [139, 10, 165], [141, 11, 165], [142, 12, 164], [143, 13, 164], [145, 14, 163], [146, 15, 163], [148, 16, 162], [149, 17, 161], [150, 19, 161], [152, 20, 160], [153, 21, 159], [154, 22, 159], [156, 23, 158], [157, 24, 157], [158, 25, 157], [160, 26, 156], [161, 27, 155], [162, 29, 154], [163, 30, 154], [165, 31, 153], [166, 32, 152], [167, 33, 151], [168, 34, 150], [170, 35, 149], [171, 36, 148], [172, 38, 148], [173, 39, 147], [174, 40, 146], [176, 41, 145], [177, 42, 144], [178, 43, 143], [179, 44, 142], [180, 46, 141], [181, 47, 140], [182, 48, 139], [183, 49, 138], [184, 50, 137], [186, 51, 136], [187, 52, 136], [188, 53, 135], [189, 55, 134], [190, 56, 133], [191, 57, 132], [192, 58, 131], [193, 59, 130], [194, 60, 129], [195, 61, 128], [196, 62, 127], [197, 64, 126], [198, 65, 125], [199, 66, 124], [200, 67, 123], [201, 68, 122], [202, 69, 122], [203, 70, 121], [204, 71, 120], [204, 73, 119], [205, 74, 118], [206, 75, 117], [207, 76, 116], [208, 77, 115], [209, 78, 114], [210, 79, 113], [211, 81, 113], [212, 82, 112], [213, 83, 111], [213, 84, 110], [214, 85, 109], [215, 86, 108], [216, 87, 107], [217, 88, 106], [218, 90, 106], [218, 91, 105], [219, 92, 104], [220, 93, 103], [221, 94, 102], [222, 95, 101], [222, 97, 100], [223, 98, 99], [224, 99, 99], [225, 100, 98], [226, 101, 97], [226, 102, 96], [227, 104, 95], [228, 105, 94], [229, 106, 93], [229, 107, 93], [230, 108, 92], [231, 110, 91], [231, 111, 90], [232, 112, 89], [233, 113, 88], [233, 114, 87], [234, 116, 87], [235, 117, 86], [235, 118, 85], [236, 119, 84], [237, 121, 83], [237, 122, 82], [238, 123, 81], [239, 124, 81], [239, 126, 80], [240, 127, 79], [240, 128, 78], [241, 129, 77], [241, 131, 76], [242, 132, 75], [243, 133, 75], [243, 135, 74], [244, 136, 73], [244, 137, 72], [245, 139, 71], [245, 140, 70], [246, 141, 69], [246, 143, 68], [247, 144, 68], [247, 145, 67], [247, 147, 66], [248, 148, 65], [248, 149, 64], [249, 151, 63], [249, 152, 62], [249, 154, 62], [250, 155, 61], [250, 156, 60], [250, 158, 59], [251, 159, 58], [251, 161, 57], [251, 162, 56], [252, 163, 56], [252, 165, 55], [252, 166, 54], [252, 168, 53], [252, 169, 52], [253, 171, 51], [253, 172, 51], [253, 174, 50], [253, 175, 49], [253, 177, 48], [253, 178, 47], [253, 180, 47], [253, 181, 46], [254, 183, 45], [254, 184, 44], [254, 186, 44], [254, 187, 43], [254, 189, 42], [254, 190, 42], [254, 192, 41], [253, 194, 41], [253, 195, 40], [253, 197, 39], [253, 198, 39], [253, 200, 39], [253, 202, 38], [253, 203, 38], [252, 205, 37], [252, 206, 37], [252, 208, 37], [252, 210, 37], [251, 211, 36], [251, 213, 36], [251, 215, 36], [250, 216, 36], [250, 218, 36], [249, 220, 36], [249, 221, 37], [248, 223, 37], [248, 225, 37], [247, 226, 37], [247, 228, 37], [246, 230, 38], [246, 232, 38], [245, 233, 38], [245, 235, 39], [244, 237, 39], [243, 238, 39], [243, 240, 39], [242, 242, 39], [241, 244, 38], [241, 245, 37], [240, 247, 36], [240, 249, 33]];
+const schemeViridis = [[68, 1, 84], [68, 2, 86], [69, 4, 87], [69, 5, 89], [70, 7, 90], [70, 8, 92], [70, 10, 93], [70, 11, 94], [71, 13, 96], [71, 14, 97], [71, 16, 99], [71, 17, 100], [71, 19, 101], [72, 20, 103], [72, 22, 104], [72, 23, 105], [72, 24, 106], [72, 26, 108], [72, 27, 109], [72, 28, 110], [72, 30, 111], [72, 31, 112], [72, 32, 113], [72, 34, 115], [72, 35, 116], [72, 36, 117], [72, 38, 118], [72, 39, 119], [72, 40, 120], [72, 42, 121], [72, 43, 122], [72, 44, 123], [72, 46, 124], [72, 47, 125], [72, 48, 126], [72, 50, 127], [72, 51, 128], [72, 52, 129], [72, 53, 130], [72, 55, 131], [72, 56, 132], [72, 57, 133], [72, 59, 134], [72, 60, 135], [72, 61, 136], [72, 63, 137], [72, 64, 137], [72, 65, 138], [72, 67, 139], [72, 68, 140], [72, 69, 141], [72, 71, 142], [72, 72, 143], [72, 73, 144], [72, 75, 145], [72, 76, 146], [72, 77, 147], [72, 79, 148], [72, 80, 149], [72, 82, 150], [72, 83, 150], [72, 84, 151], [72, 86, 152], [72, 87, 153], [72, 88, 154], [72, 90, 155], [71, 91, 156], [71, 92, 157], [71, 94, 158], [71, 95, 158], [71, 97, 159], [71, 98, 160], [71, 99, 161], [71, 101, 162], [71, 102, 163], [71, 103, 164], [71, 105, 164], [71, 106, 165], [71, 108, 166], [71, 109, 167], [71, 110, 168], [71, 112, 169], [71, 113, 169], [71, 114, 170], [71, 116, 171], [71, 117, 172], [70, 119, 173], [70, 120, 174], [70, 121, 174], [70, 123, 175], [70, 124, 176], [70, 125, 177], [70, 127, 178], [70, 128, 178], [70, 130, 179], [70, 131, 180], [70, 132, 181], [70, 134, 182], [70, 135, 182], [70, 136, 183], [70, 138, 184], [70, 139, 185], [70, 141, 186], [70, 142, 186], [70, 143, 187], [70, 145, 188], [70, 146, 189], [70, 148, 189], [70, 149, 190], [70, 150, 191], [70, 152, 192], [70, 153, 192], [70, 155, 193], [70, 156, 194], [70, 157, 195], [70, 159, 195], [70, 160, 196], [70, 162, 197], [70, 163, 198], [70, 164, 198], [70, 166, 199], [70, 167, 200], [71, 169, 200], [71, 170, 201], [71, 171, 202], [71, 173, 203], [71, 174, 203], [71, 176, 204], [71, 177, 205], [71, 178, 205], [72, 180, 206], [72, 181, 207], [72, 183, 207], [72, 184, 208], [73, 185, 209], [73, 187, 209], [73, 188, 210], [74, 190, 211], [74, 191, 211], [74, 192, 212], [75, 194, 213], [75, 195, 213], [76, 197, 214], [76, 198, 214], [77, 199, 215], [77, 201, 216], [78, 202, 216], [78, 204, 217], [79, 205, 217], [79, 207, 218], [80, 208, 218], [81, 209, 219], [81, 211, 220], [82, 212, 220], [83, 214, 221], [83, 215, 221], [84, 216, 222], [85, 218, 222], [85, 219, 223], [86, 221, 223], [87, 222, 224], [88, 224, 224], [88, 225, 225], [89, 226, 225], [90, 228, 226], [91, 229, 226], [92, 231, 227], [92, 232, 227], [93, 234, 228], [94, 235, 228], [95, 236, 229], [96, 238, 229], [97, 239, 230], [97, 241, 230], [98, 242, 231], [99, 244, 231], [100, 245, 232], [101, 246, 232], [102, 248, 233], [103, 249, 233], [104, 251, 234], [105, 252, 234]];
+const schemeJet = Array.from({ length: 256 }, (_, i2) => {
+  const t4 = i2 / 255;
+  let r3;
+  let g2;
+  let b2;
+  if (t4 < 0.125) {
+    r3 = 0;
+    g2 = 0;
+    b2 = 0.5 + t4 * 4;
+  } else if (t4 < 0.375) {
+    r3 = 0;
+    g2 = (t4 - 0.125) * 4;
+    b2 = 1;
+  } else if (t4 < 0.625) {
+    r3 = (t4 - 0.375) * 4;
+    g2 = 1;
+    b2 = 1 - (t4 - 0.375) * 4;
+  } else if (t4 < 0.875) {
+    r3 = 1;
+    g2 = 1 - (t4 - 0.625) * 4;
+    b2 = 0;
+  } else {
+    r3 = 1 - (t4 - 0.875) * 4;
+    g2 = 0;
+    b2 = 0;
+  }
+  return [Math.round(r3 * 255), Math.round(g2 * 255), Math.round(b2 * 255)];
+});
+const schemeGreys = Array.from({ length: 256 }, (_, i2) => [i2, i2, i2]);
 function rgbSpline$1(spline) {
   return (colors2) => {
     const n2 = colors2.length;
@@ -18203,7 +18248,15 @@ function basis$2(values2) {
   };
 }
 const interpolateRgbBasis = rgbSpline$1(basis$2);
+function interpolateSequentialMulti(range2) {
+  const n2 = range2.length;
+  return (t4) => range2[Math.max(0, Math.min(n2 - 1, Math.floor(t4 * n2)))];
+}
 interpolateRgbBasis(schemeRdBu);
+interpolateSequentialMulti(schemePlasma);
+interpolateSequentialMulti(schemeViridis);
+interpolateSequentialMulti(schemeJet);
+interpolateSequentialMulti(schemeGreys);
 function stratifyExpressionData(sampleEdges, sampleSets, sampleSetSelection, expressionData, obsIndex, mergedCellSets, geneSelection, cellSetSelection, cellSetColor, featureValueTransform, featureValueTransformCoefficient) {
   const result = new InternMap2([], JSON.stringify);
   const hasSampleSetSelection = Array.isArray(sampleSetSelection) && sampleSetSelection.length > 0;
@@ -178658,22 +178711,22 @@ function addDecoder(cases2, importFn) {
   }
   cases2.forEach((c2) => registry$1.set(c2, importFn));
 }
-addDecoder([void 0, 1], () => import("./raw-B-zQvZxn.js").then((m2) => m2.default));
-addDecoder(5, () => import("./lzw-BXBJRSoa.js").then((m2) => m2.default));
+addDecoder([void 0, 1], () => import("./raw-CCURUeAu.js").then((m2) => m2.default));
+addDecoder(5, () => import("./lzw-DQkfb7of.js").then((m2) => m2.default));
 addDecoder(6, () => {
   throw new Error("old style JPEG compression is not supported.");
 });
-addDecoder(7, () => import("./jpeg-BcFUc49m.js").then((m2) => m2.default));
-addDecoder([8, 32946], () => import("./deflate-DW1iET8g.js").then((m2) => m2.default));
-addDecoder(32773, () => import("./packbits-C5DpT4rK.js").then((m2) => m2.default));
+addDecoder(7, () => import("./jpeg-DA0bMpPw.js").then((m2) => m2.default));
+addDecoder([8, 32946], () => import("./deflate-DN9irvtS.js").then((m2) => m2.default));
+addDecoder(32773, () => import("./packbits-CuaN4bB2.js").then((m2) => m2.default));
 addDecoder(
   34887,
-  () => import("./lerc-DvHuJtok.js").then(async (m2) => {
+  () => import("./lerc-PCO9t4ZR.js").then(async (m2) => {
     await m2.zstd.init();
     return m2;
   }).then((m2) => m2.default)
 );
-addDecoder(50001, () => import("./webimage-B3lyoOmq.js").then((m2) => m2.default));
+addDecoder(50001, () => import("./webimage-CUTBnRFx.js").then((m2) => m2.default));
 function decodeRowAcc(row, stride) {
   let length2 = row.length - stride;
   let offset2 = 0;
@@ -197818,7 +197871,7 @@ function useFilteredVolcanoData(props) {
       const rawSampleSetPathB = coordinationValues.sampleSetFilter[1];
       const sampleSetPathB = [...rawSampleSetPathB];
       sampleSetPathB[0] = sampleSetsColumnNameMappingReversed[rawSampleSetPathB[0]];
-      if (isEqual$3(sampleSetPathA, sampleSetSelection[1]) && isEqual$3(sampleSetPathB, sampleSetSelection[0])) {
+      if (isEqual$3(sampleSetPathA, sampleSetSelection[0]) && isEqual$3(sampleSetPathB, sampleSetSelection[1])) {
         shouldSwapFoldChangeDirection = true;
       }
     }
@@ -250744,6 +250797,10 @@ function TreemapSubscriber(props) {
     /* @__PURE__ */ React__default.createElement("div", { style: { position: "absolute", right: "2px", bottom: "2px", fontSize: "10px" } }, unselectedObsCount > 0 ? /* @__PURE__ */ React__default.createElement("span", null, `${commaNumber(unselectedObsCount)} ${pluralize(obsType, unselectedObsCount)} from ${commaNumber(unselectedSampleCount)} ${pluralize(sampleType, unselectedSampleCount)} currently omitted`) : null)
   );
 }
+const GOLDEN_RATIO = 0.6180339887498948;
+function topJitter(index2, rangePixels) {
+  return index2 * GOLDEN_RATIO % 1 * rangePixels;
+}
 function VolcanoPlot(props) {
   const {
     theme,
@@ -250833,10 +250890,10 @@ function VolcanoPlot(props) {
       const obsSetPath = [...rawObsSetPath];
       obsSetPath[0] = obsSetsColumnNameMappingReversed[rawObsSetPath[0]];
       const color2 = obsSetColorScale(obsSetPath);
-      obsSetG.append("g").selectAll("circle").data(filteredDf).join("circle").attr("cx", (d) => xScale(d.logFoldChange)).attr("cy", (d) => yScale(d.minusLog10p)).attr("r", 3).attr("opacity", 0.5).attr("fill", color2).on("click", (event2, d) => {
+      obsSetG.append("g").selectAll("circle").data(filteredDf).join("circle").attr("cx", (d) => xScale(d.logFoldChange)).attr("cy", (d, i2) => yScale(d.minusLog10p) + (!Number.isFinite(d.minusLog10p) ? topJitter(i2, 20) : 0)).attr("r", 3).attr("opacity", 0.5).attr("fill", color2).on("click", (event2, d) => {
         onFeatureClick(d.featureId);
       });
-      const textElements = obsSetG.append("g").selectAll("text").data(filteredDf).join("text").text((d) => d.featureId).attr("text-anchor", (d) => d.logFoldChange < 0 ? "end" : "start").attr("x", (d) => xScale(d.logFoldChange)).attr("y", (d) => yScale(d.minusLog10p)).style("display", (d) => Math.abs(d.logFoldChange) < (featureLabelFoldChangeThreshold ?? 5) || d.featureSignificance >= (featureLabelSignificanceThreshold ?? 0.01) ? "none" : void 0).attr("fill", color2).on("click", (event2, d) => {
+      const textElements = obsSetG.append("g").selectAll("text").data(filteredDf).join("text").text((d) => d.featureId).attr("text-anchor", (d) => d.logFoldChange < 0 ? "end" : "start").attr("x", (d) => xScale(d.logFoldChange)).attr("y", (d, i2) => yScale(d.minusLog10p) + (!Number.isFinite(d.minusLog10p) ? topJitter(i2, 20) : 0)).style("display", (d) => Math.abs(d.logFoldChange) < (featureLabelFoldChangeThreshold ?? 5) || d.featureSignificance >= (featureLabelSignificanceThreshold ?? 0.01) ? "none" : void 0).attr("fill", color2).on("click", (event2, d) => {
         onFeatureClick(d.featureId);
       });
       textElements.append("title").text((d) => `${featureType}: ${d.featureId}

package/dist/index.js

@@ -1,4 +1,4 @@
-import { b, f, C, e, a, i, D, h, E, F, c, d, T, V } from "./index-DKGZofDL.js";
+import { b, f, C, e, a, i, D, h, E, F, c, d, T, V } from "./index-DKWiD0_-.js";
 export {
   b as CellSetCompositionBarPlotSubscriber,
   f as CellSetExpressionPlot,

package/dist/{jpeg-BcFUc49m.js → jpeg-DA0bMpPw.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-DKGZofDL.js";
+import { B as BaseDecoder } from "./index-DKWiD0_-.js";
 const dctZigZag = new Int32Array([
   0,
   1,

package/dist/{lerc-DvHuJtok.js → lerc-PCO9t4ZR.js}

@@ -1,5 +1,5 @@
 import { i as inflate_1 } from "./pako.esm-SxljTded.js";
-import { g as getDefaultExportFromCjs, B as BaseDecoder } from "./index-DKGZofDL.js";
+import { g as getDefaultExportFromCjs, B as BaseDecoder } from "./index-DKWiD0_-.js";
 const LercParameters = {
   AddCompression: 1
 };

package/dist/{lzw-BXBJRSoa.js → lzw-DQkfb7of.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-DKGZofDL.js";
+import { B as BaseDecoder } from "./index-DKWiD0_-.js";
 const MIN_BITS = 9;
 const CLEAR_CODE = 256;
 const EOI_CODE = 257;

package/dist/{packbits-C5DpT4rK.js → packbits-CuaN4bB2.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-DKGZofDL.js";
+import { B as BaseDecoder } from "./index-DKWiD0_-.js";
 class PackbitsDecoder extends BaseDecoder {
   decodeBlock(buffer) {
     const dataView = new DataView(buffer);

package/dist/{raw-B-zQvZxn.js → raw-CCURUeAu.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-DKGZofDL.js";
+import { B as BaseDecoder } from "./index-DKWiD0_-.js";
 class RawDecoder extends BaseDecoder {
   decodeBlock(buffer) {
     return buffer;

package/dist/{webimage-B3lyoOmq.js → webimage-CUTBnRFx.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-DKGZofDL.js";
+import { B as BaseDecoder } from "./index-DKWiD0_-.js";
 class WebImageDecoder extends BaseDecoder {
   constructor() {
     super();

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

@@ -1 +1 @@
-{"version":3,"file":"VolcanoPlot.d.ts","sourceRoot":"","sources":["../src/VolcanoPlot.js"],"names":[],"mappings":"AAWA,qDAgQC"}
+{"version":3,"file":"VolcanoPlot.d.ts","sourceRoot":"","sources":["../src/VolcanoPlot.js"],"names":[],"mappings":"AAmBA,qDAgQC"}

package/dist-tsc/VolcanoPlot.js

@@ -9,6 +9,13 @@ import { select } from 'd3-selection';
 import { capitalize, getDefaultForegroundColor } from '@vitessce/utils';
 import { colorArrayToString } from '@vitessce/sets-utils';
 import { getColorScale, useFilteredVolcanoData } from './utils.js';
+// Deterministic jitter for points clamped at the top of the y-axis.
+// Uses the golden-ratio sequence (index * φ mod 1) which is optimally
+// equidistributed — no clustering regardless of how many points there are.
+const GOLDEN_RATIO = 0.6180339887498948;
+function topJitter(index, rangePixels) {
+    return ((index * GOLDEN_RATIO) % 1) * rangePixels;
+}
 export default function VolcanoPlot(props) {
     const { theme, width, height, obsType, featureType, obsSetsColumnNameMappingReversed, sampleSetsColumnNameMappingReversed, sampleSetSelection, obsSetSelection, obsSetColor, sampleSetColor, data, marginTop = 5, marginRight = 5, marginLeft = 50, marginBottom = 50, onFeatureClick, featurePointSignificanceThreshold, featurePointFoldChangeThreshold, featureLabelSignificanceThreshold, featureLabelFoldChangeThreshold, } = props;
     const svgRef = useRef();
@@ -157,7 +164,7 @@ export default function VolcanoPlot(props) {
                 .data(filteredDf)
                 .join('circle')
                 .attr('cx', d => xScale(d.logFoldChange))
-                .attr('cy', d => yScale(d.minusLog10p))
+                .attr('cy', (d, i) => yScale(d.minusLog10p) + (!Number.isFinite(d.minusLog10p) ? topJitter(i, 20) : 0))
                 .attr('r', 3)
                 .attr('opacity', 0.5)
                 .attr('fill', color)
@@ -171,7 +178,7 @@ export default function VolcanoPlot(props) {
                 .text(d => d.featureId)
                 .attr('text-anchor', d => (d.logFoldChange < 0 ? 'end' : 'start'))
                 .attr('x', d => xScale(d.logFoldChange))
-                .attr('y', d => yScale(d.minusLog10p))
+                .attr('y', (d, i) => yScale(d.minusLog10p) + (!Number.isFinite(d.minusLog10p) ? topJitter(i, 20) : 0))
                 .style('display', d => ((Math.abs(d.logFoldChange) < (featureLabelFoldChangeThreshold ?? 5.0)
                 || (d.featureSignificance >= (featureLabelSignificanceThreshold ?? 0.01))) ? 'none' : undefined))
                 .attr('fill', color)

package/dist-tsc/VolcanoPlot.js.map

@@ -1 +1 @@
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package/dist-tsc/utils.js

@@ -63,8 +63,8 @@ export function useFilteredVolcanoData(props) {
             const rawSampleSetPathB = coordinationValues.sampleSetFilter[1];
             const sampleSetPathB = [...rawSampleSetPathB];
             sampleSetPathB[0] = sampleSetsColumnNameMappingReversed[rawSampleSetPathB[0]];
-            if (isEqual(sampleSetPathA, sampleSetSelection[1])
-                && isEqual(sampleSetPathB, sampleSetSelection[0])) {
+            if (isEqual(sampleSetPathA, sampleSetSelection[0])
+                && isEqual(sampleSetPathB, sampleSetSelection[1])) {
                 shouldSwapFoldChangeDirection = true;
             }
         }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@vitessce/statistical-plots",
-  "version": "4.0.0",
+  "version": "4.0.2",
   "author": "HIDIVE Lab at HMS",
   "homepage": "http://vitessce.io",
   "repository": {
@@ -28,13 +28,13 @@
     "react-aria": "^3.47.0",
     "internmap": "^2.0.3",
     "uuid": "^9.0.0",
-    "@vitessce/styles": "4.0.0",
-    "@vitessce/constants-internal": "4.0.0",
-    "@vitessce/sets-utils": "4.0.0",
-    "@vitessce/vega": "4.0.0",
-    "@vitessce/utils": "4.0.0",
-    "@vitessce/vit-s": "4.0.0",
-    "@vitessce/gl": "4.0.0"
+    "@vitessce/constants-internal": "4.0.2",
+    "@vitessce/styles": "4.0.2",
+    "@vitessce/vega": "4.0.2",
+    "@vitessce/sets-utils": "4.0.2",
+    "@vitessce/vit-s": "4.0.2",
+    "@vitessce/gl": "4.0.2",
+    "@vitessce/utils": "4.0.2"
   },
   "devDependencies": {
     "react": "19.2.6",

package/src/VolcanoPlot.js

@@ -9,6 +9,14 @@ import { capitalize, getDefaultForegroundColor } from '@vitessce/utils';
 import { colorArrayToString } from '@vitessce/sets-utils';
 import { getColorScale, useFilteredVolcanoData } from './utils.js';
 
+// Deterministic jitter for points clamped at the top of the y-axis.
+// Uses the golden-ratio sequence (index * φ mod 1) which is optimally
+// equidistributed — no clustering regardless of how many points there are.
+const GOLDEN_RATIO = 0.6180339887498948;
+function topJitter(index, rangePixels) {
+  return ((index * GOLDEN_RATIO) % 1) * rangePixels;
+}
+
 export default function VolcanoPlot(props) {
   const {
     theme,
@@ -215,7 +223,7 @@ export default function VolcanoPlot(props) {
         .data(filteredDf)
         .join('circle')
           .attr('cx', d => xScale(d.logFoldChange))
-          .attr('cy', d => yScale(d.minusLog10p))
+          .attr('cy', (d, i) => yScale(d.minusLog10p) + (!Number.isFinite(d.minusLog10p) ? topJitter(i, 20) : 0))
           .attr('r', 3)
           .attr('opacity', 0.5)
           .attr('fill', color)
@@ -230,7 +238,7 @@ export default function VolcanoPlot(props) {
           .text(d => d.featureId)
           .attr('text-anchor', d => (d.logFoldChange < 0 ? 'end' : 'start'))
           .attr('x', d => xScale(d.logFoldChange))
-          .attr('y', d => yScale(d.minusLog10p))
+          .attr('y', (d, i) => yScale(d.minusLog10p) + (!Number.isFinite(d.minusLog10p) ? topJitter(i, 20) : 0))
           .style('display', d => ((
             Math.abs(d.logFoldChange) < (featureLabelFoldChangeThreshold ?? 5.0)
             || (d.featureSignificance >= (featureLabelSignificanceThreshold ?? 0.01))

package/src/utils.js

@@ -87,8 +87,8 @@ export function useFilteredVolcanoData(props) {
       sampleSetPathB[0] = sampleSetsColumnNameMappingReversed[rawSampleSetPathB[0]];
 
       if (
-        isEqual(sampleSetPathA, sampleSetSelection[1])
-        && isEqual(sampleSetPathB, sampleSetSelection[0])
+        isEqual(sampleSetPathA, sampleSetSelection[0])
+        && isEqual(sampleSetPathB, sampleSetSelection[1])
       ) {
         shouldSwapFoldChangeDirection = true;
       }