@vitessce/statistical-plots 4.0.0 → 4.0.1

package/dist/{deflate-DW1iET8g.js → deflate-CqV6y5ls.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-Do9Ri4cE.js";
 class DeflateDecoder extends BaseDecoder {
   decodeBlock(buffer) {
     return inflate_1(new Uint8Array(buffer)).buffer;

package/dist/{index-DKGZofDL.js → index-Do9Ri4cE.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,
@@ -178658,22 +178661,22 @@ 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-CxnSBy3Z.js").then((m2) => m2.default));
+addDecoder(5, () => import("./lzw-DzurT5M0.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-CsJnGGfB.js").then((m2) => m2.default));
+addDecoder([8, 32946], () => import("./deflate-CqV6y5ls.js").then((m2) => m2.default));
+addDecoder(32773, () => import("./packbits-AHl4dCuO.js").then((m2) => m2.default));
 addDecoder(
   34887,
-  () => import("./lerc-DvHuJtok.js").then(async (m2) => {
+  () => import("./lerc-BZ3Pqm18.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-DgIqTO3W.js").then((m2) => m2.default));
 function decodeRowAcc(row, stride) {
   let length2 = row.length - stride;
   let offset2 = 0;
@@ -197818,7 +197821,7 @@ 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$3(sampleSetPathB, sampleSetSelection[1])) {
         shouldSwapFoldChangeDirection = true;
       }
     }
@@ -250744,6 +250747,10 @@ function TreemapSubscriber(props) {
     /* @__PURE__ */ React__default.createElement("div", { style: { position: "absolute", right: "2px", bottom: "2px", fontSize: "10px" } }, unselectedObsCount > 0 ? /* @__PURE__ */ React__default.createElement("span", null, `${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 +250840,10 @@ 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-Do9Ri4cE.js";
 export {
   b as CellSetCompositionBarPlotSubscriber,
   f as CellSetExpressionPlot,

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

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-DKGZofDL.js";
+import { B as BaseDecoder } from "./index-Do9Ri4cE.js";
 const dctZigZag = new Int32Array([
   0,
   1,

package/dist/{lerc-DvHuJtok.js → lerc-BZ3Pqm18.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-Do9Ri4cE.js";
 const LercParameters = {
   AddCompression: 1
 };

package/dist/{lzw-BXBJRSoa.js → lzw-DzurT5M0.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-DKGZofDL.js";
+import { B as BaseDecoder } from "./index-Do9Ri4cE.js";
 const MIN_BITS = 9;
 const CLEAR_CODE = 256;
 const EOI_CODE = 257;

package/dist/{packbits-C5DpT4rK.js → packbits-AHl4dCuO.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-DKGZofDL.js";
+import { B as BaseDecoder } from "./index-Do9Ri4cE.js";
 class PackbitsDecoder extends BaseDecoder {
   decodeBlock(buffer) {
     const dataView = new DataView(buffer);

package/dist/{raw-B-zQvZxn.js → raw-CxnSBy3Z.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-DKGZofDL.js";
+import { B as BaseDecoder } from "./index-Do9Ri4cE.js";
 class RawDecoder extends BaseDecoder {
   decodeBlock(buffer) {
     return buffer;

package/dist/{webimage-B3lyoOmq.js → webimage-DgIqTO3W.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-DKGZofDL.js";
+import { B as BaseDecoder } from "./index-Do9Ri4cE.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

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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": "4.0.1",
   "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/styles": "4.0.1",
+    "@vitessce/constants-internal": "4.0.1",
+    "@vitessce/sets-utils": "4.0.1",
+    "@vitessce/utils": "4.0.1",
+    "@vitessce/vega": "4.0.1",
+    "@vitessce/gl": "4.0.1",
+    "@vitessce/vit-s": "4.0.1"
   },
   "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;
       }