@inflexa-ai/harness 0.45.1 → 0.46.2

package/dist/report-render/figures/locuszoom.js

@@ -115,6 +115,7 @@ const GENE_LINE_PLACE = 0.25;
 const GENE_CHARACTER_SHARE = 0.6;
 const GENE_GAP_CHARACTERS = 1;
 /** The trailing unit of a declared position label, which the megabase axis replaces. */
+// oxlint-disable-next-line eslint-js/no-restricted-syntax -- the declared unit suffix (bp, base pairs, kb, Mb) in its parenthesised form, stripped with the whitespace around it.
 const POSITION_UNIT = /\s*\((bp|base pairs|kb|Mb)\)\s*$/i;
 function deriveLocusZoom(block, rows, context) {
     const columns = locusColumns(block, rows, context);
@@ -124,16 +125,16 @@ function deriveLocusZoom(block, rows, context) {
     const xs = rows.map((row) => toNumber(row[position]));
     const faulty = xs.findIndex((x) => x === null);
     if (faulty >= 0) {
-        return err(chartProblem(context.blockId, `The locuszoom reads the "${position}" column as a position in base pairs, and row ${faulty + 1} holds "${String(rows[faulty][position] ?? "")}", which is not a number.`));
+        return err(chartProblem(context.blockId, `The locuszoom reads the "${position}" column as a position in base pairs, and row ${faulty + 1} holds "${String(rows[faulty]?.[position] ?? "")}", which is not a number.`));
     }
     const chromosomes = chromosome === undefined ? [] : distinctNames(rows, chromosome);
     if (chromosomes.length > 1) {
-        return err(chartProblem(context.blockId, `The locuszoom draws one region of one chromosome, and the "${chromosome}" column holds "${chromosomes[0]}" and "${chromosomes[1]}".`));
+        return err(chartProblem(context.blockId, `The locuszoom draws one region of one chromosome, and the "${String(chromosome)}" column holds "${String(chromosomes[0])}" and "${String(chromosomes[1])}".`));
     }
     const r2s = rows.map((row) => toNumber(row[r2]));
     const outside = r2s.findIndex((value) => value !== null && (value < 0 || value > 1));
     if (outside >= 0) {
-        return err(chartProblem(context.blockId, `The locuszoom reads the "${r2}" column as the r² with the lead variant, and row ${outside + 1} holds ${r2s[outside]}, which is outside 0 to 1.`));
+        return err(chartProblem(context.blockId, `The locuszoom reads the "${r2}" column as the r² with the lead variant, and row ${outside + 1} holds ${String(r2s[outside])}, which is outside 0 to 1.`));
     }
     const line = -Math.log10(MANHATTAN_P_THRESHOLD);
     const finite = transformColumn(rows, p, "neg_log10");
@@ -151,7 +152,7 @@ function deriveLocusZoom(block, rows, context) {
     const lanes = genes.value === undefined ? 0 : Math.max(1, (largest(genes.value.map((gene) => gene.lane)) ?? 0) + 1);
     const composition = {
         series: [
-            { form: "scatter", encoding: { x: position, y: { column: p, transform: "neg_log10" }, color: r2, ...(label !== undefined ? { label } : {}) } },
+            { form: "scatter", encoding: { x: position, y: { column: p, transform: "neg_log10" }, color: r2, label } },
             ...(rate !== undefined ? [{ form: "line", name: RECOMBINATION_NAME, encoding: { x: position, y: rate } }] : []),
         ],
         annotations: [{ kind: "reference-line", axis: "y", value: line }],
@@ -163,17 +164,17 @@ function deriveLocusZoom(block, rows, context) {
     const option = composed.value;
     const [points, recombination] = seriesOf(option);
     const nameOf = (index) => {
-        const cell = label === undefined ? undefined : rows[index][label];
-        return cell === undefined || cell === null || String(cell).trim() === "" ? undefined : String(cell);
+        const cell = label === undefined ? undefined : rows[index]?.[label];
+        return cell === undefined || String(cell).trim() === "" ? undefined : String(cell);
     };
     const item = (index, y) => {
         const name = nameOf(index);
-        return { ...(name !== undefined ? { name } : {}), value: [xs[index] ?? 0, y] };
+        return { name, value: [xs[index] ?? 0, y] };
     };
     const missing = [];
     for (let index = 0; index < rows.length; index += 1) {
         const y = finite[index];
-        if (r2s[index] === null && y !== null)
+        if (r2s[index] === null && y !== null && y !== undefined)
             missing.push(item(index, y));
     }
     const rated = rate === undefined ? [] : ratesInOrder(rows, xs, rate);
@@ -213,7 +214,7 @@ function deriveLocusZoom(block, rows, context) {
             ]
             : []),
         ...(missing.length > 0 ? [missingSeries(missing)] : []),
-        ...(zeroRows.length > 0 ? [zeroSeries(zeroRows.map((index) => ({ ...item(index, zeroY), itemStyle: { color: binColor(r2s[index]) } })))] : []),
+        ...(zeroRows.length > 0 ? [zeroSeries(zeroRows.map((index) => ({ ...item(index, zeroY), itemStyle: { color: binColor(r2s[index] ?? null) } })))] : []),
         tickSeries(window),
         guideSeries(guideText(MANHATTAN_P_THRESHOLD), line, { ys, xs, rated, top, rateTop, window, layout }),
         ...(lead !== undefined ? [leadSeries(item(lead, ys[lead] ?? 0))] : []),
@@ -250,16 +251,20 @@ function locusColumns(block, rows, context) {
             return err(chartProblem(context.blockId, `The locuszoom reads the "${name}" column as it stands, thus the channel takes no transform and no "orderBy".`));
         }
     }
+    const metric = encoding.metric;
+    const group = encoding.group;
     const found = {
         position: channelColumn(x.value),
         // The figure applies the transform of the p column itself, as the Manhattan figure does.
         p: channelColumn(y.value),
         r2: channelColumn(encoding.color),
-        ...(encoding.label !== undefined ? { label: encoding.label } : {}),
-        ...(encoding.metric !== undefined ? { rate: channelColumn(encoding.metric) } : {}),
-        ...(encoding.group !== undefined ? { chromosome: channelColumn(encoding.group) } : {}),
+        label: encoding.label,
+        rate: metric === undefined ? undefined : channelColumn(metric),
+        chromosome: group === undefined ? undefined : channelColumn(group),
     };
-    for (const column of Object.values(found)) {
+    for (const column of [found.position, found.p, found.r2, found.label, found.rate, found.chromosome]) {
+        if (column === undefined)
+            continue;
         if (rows.length > 0 && !columnPresent(column, rows, context.columns)) {
             return err(chartProblem(context.blockId, `The column "${column}" is absent from every row.`));
         }
@@ -271,7 +276,7 @@ function distinctNames(rows, column) {
     const names = [];
     for (const row of rows) {
         const cell = row[column];
-        if (cell === undefined || cell === null || String(cell).trim() === "")
+        if (cell === undefined || String(cell).trim() === "")
             continue;
         const name = categoryName(cell);
         if (!names.includes(name))
@@ -290,7 +295,7 @@ function leadRow(xs, finite, zeros) {
     let best = Number.NEGATIVE_INFINITY;
     for (let index = 0; index < finite.length; index += 1) {
         const rank = zeros.has(index) ? Number.POSITIVE_INFINITY : finite[index];
-        if (rank === null)
+        if (rank === null || rank === undefined)
             continue;
         if (lead === undefined || rank > best || (rank === best && (xs[index] ?? 0) < (xs[lead] ?? 0))) {
             lead = index;
@@ -309,7 +314,7 @@ function ratesInOrder(rows, xs, rate) {
     for (const [index, row] of rows.entries()) {
         const x = xs[index];
         const value = toNumber(row[rate]);
-        if (x !== null && value !== null)
+        if (x !== null && x !== undefined && value !== null)
             pairs.push([x, value]);
     }
     return pairs.sort((a, b) => a[0] - b[0]);
@@ -339,17 +344,21 @@ function guideStart(text, line, room) {
     const blocked = [];
     for (const [index, x] of room.xs.entries()) {
         const y = room.ys[index];
-        if (x !== null && y !== null && y + reach >= low && y - reach <= high)
+        if (x !== null && y !== null && y !== undefined && y + reach >= low && y - reach <= high)
             blocked.push([x - half, x + half]);
     }
     if (room.rateTop > 0) {
         const rateLow = (low / room.top) * room.rateTop;
         const rateHigh = (high / room.top) * room.rateTop;
-        for (let index = 1; index < room.rated.length; index += 1) {
-            const [x1, r1] = room.rated[index - 1];
-            const [x2, r2] = room.rated[index];
-            if (Math.max(r1, r2) >= rateLow && Math.min(r1, r2) <= rateHigh)
-                blocked.push([x1, x2]);
+        let previous;
+        for (const pair of room.rated) {
+            if (previous !== undefined) {
+                const [x1, r1] = previous;
+                const [x2, r2] = pair;
+                if (Math.max(r1, r2) >= rateLow && Math.min(r1, r2) <= rateHigh)
+                    blocked.push([x1, x2]);
+            }
+            previous = pair;
         }
     }
     const marks = union(blocked);
@@ -387,13 +396,16 @@ function union(intervals) {
 function coverage(marks) {
     const before = [0];
     for (const [start, end] of marks)
-        before.push(before[before.length - 1] + end - start);
+        before.push((before[before.length - 1] ?? 0) + end - start);
     const firstEndingAfter = (x) => {
         let low = 0;
         let high = marks.length;
         while (low < high) {
             const middle = (low + high) >> 1;
-            if (marks[middle][1] > x)
+            const mark = marks[middle];
+            if (mark === undefined)
+                break;
+            if (mark[1] > x)
                 high = middle;
             else
                 low = middle + 1;
@@ -403,11 +415,18 @@ function coverage(marks) {
     return (from, to) => {
         const first = firstEndingAfter(from);
         let last = firstEndingAfter(to);
-        if (last < marks.length && marks[last][0] < to)
+        const next = marks[last];
+        if (next !== undefined && next[0] < to)
             last += 1;
         if (first >= last)
             return 0;
-        return before[last] - before[first] - Math.max(0, from - marks[first][0]) - Math.max(0, marks[last - 1][1] - to);
+        const startMark = marks[first];
+        const endMark = marks[last - 1];
+        const startSum = before[first];
+        const endSum = before[last];
+        if (startMark === undefined || endMark === undefined || startSum === undefined || endSum === undefined)
+            return 0;
+        return endSum - startSum - Math.max(0, from - startMark[0]) - Math.max(0, endMark[1] - to);
     };
 }
 /**
@@ -451,8 +470,13 @@ function positionWindow(xs) {
     }
     const from = low ?? 0;
     const to = high ?? 0;
-    const span = Math.max(to - from, POSITION_STEPS[0]);
-    const step = POSITION_STEPS.find((candidate) => span / candidate <= POSITION_TICK_COUNT) ?? POSITION_STEPS[POSITION_STEPS.length - 1];
+    const smallest = POSITION_STEPS[0];
+    const widest = POSITION_STEPS[POSITION_STEPS.length - 1];
+    if (smallest === undefined || widest === undefined) {
+        return { min: from, max: Math.max(to, from + 1), step: 1 };
+    }
+    const span = Math.max(to - from, smallest);
+    const step = POSITION_STEPS.find((candidate) => span / candidate <= POSITION_TICK_COUNT) ?? widest;
     return { min: from, max: Math.max(to, from + 1), step };
 }
 /**
@@ -465,7 +489,7 @@ function positionTitle(context, column, chromosome) {
         return `${declared.replace(POSITION_UNIT, "")} (Mb)`;
     if (chromosome === undefined)
         return "Position (Mb)";
-    const name = chromosome.replace(/^chr/i, "");
+    const name = chromosome.toLowerCase().startsWith("chr") ? chromosome.slice(3) : chromosome;
     return `Position on chr${name} (Mb)`;
 }
 /**
@@ -504,7 +528,10 @@ function decimalsOf(step) {
 function binColor(r2) {
     if (r2 === null)
         return LD_MISSING_COLOR;
-    return (LD_BINS.find((bin, place) => r2 >= bin.low && (r2 < bin.high || place === LD_BINS.length - 1)) ?? LD_BINS[0]).color;
+    const first = LD_BINS[0];
+    if (first === undefined)
+        return LD_MISSING_COLOR;
+    return (LD_BINS.find((bin, place) => r2 >= bin.low && (r2 < bin.high || place === LD_BINS.length - 1)) ?? first).color;
 }
 /**
  * The legend of the LD bins: a piecewise map over the r² of the points, highest bin first, with the gray entry
@@ -517,7 +544,8 @@ function binColor(r2) {
 function ldLegend() {
     const bins = [...LD_BINS].reverse().map((bin, place) => ({
         gte: bin.low,
-        ...(place === 0 ? { lte: bin.high } : { lt: bin.high }),
+        lte: place === 0 ? bin.high : undefined,
+        lt: place === 0 ? undefined : bin.high,
         label: `${bin.low}–${bin.high}`,
         color: bin.color,
     }));

package/dist/report-render/figures/lollipop.js

@@ -11,6 +11,7 @@
  * box is one row of the track, and the lane of a box is the first lane where it overlaps no earlier box, thus
  * the lanes follow the order of the track rows.
  */
+import { textOf } from "../../lib/unknown-text.js";
 import { err, ok } from "neverthrow";
 import { channelColumn, channelOrder, channelTransform } from "../../contracts/report-blocks.js";
 import { STEM_RENDERER } from "../chart-renderers.js";
@@ -77,7 +78,7 @@ function deriveLollipop(block, rows, context) {
     const stemTitle = valueAxisTitle(context.labels, count.value, COUNT_TITLE);
     const series = group === undefined
         ? [stemSeries(stemTitle, CHART_PALETTE[0], stems, label)]
-        : classes.map((name, index) => stemSeries(categoryName(name), colors[index], stems.filter((stem) => classOf(stem.row, group) === name), label));
+        : classes.map((name, index) => stemSeries(categoryName(name), colors[index] ?? CHART_PALETTE[0], stems.filter((stem) => classOf(stem.row, group) === name), label));
     if (label !== undefined)
         series.push(labelSeries(stems, label));
     const positionTitle = valueAxisTitle(context.labels, position.value, POSITION_TITLE);
@@ -87,7 +88,7 @@ function deriveLollipop(block, rows, context) {
         itemWidth: LEGEND_ICON_PX,
         itemHeight: LEGEND_ICON_PX,
         itemGap: LEGEND_GAP_PX,
-        data: series.filter((entry) => entry.renderItem === STEM_RENDERER).map((entry) => String(entry.name)),
+        data: series.filter((entry) => entry.renderItem === STEM_RENDERER).map((entry) => textOf(entry.name)),
     };
     if (boxes.value === undefined) {
         return ok({ tooltip: { trigger: "item" }, xAxis: valueAxis("x", positionTitle, { min: 0, max: length }), yAxis: countAxis, series, legend });

package/dist/report-render/figures/ma.js

@@ -43,7 +43,7 @@ function maClassification(rows, pColumn, pTitle, cut) {
         categoryOf: (x, y, index) => {
             if (x === null || y === null || x <= 0)
                 return undefined;
-            const p = toNumber(rows[index][pColumn]);
+            const p = toNumber(rows[index]?.[pColumn]);
             return p !== null && p < cut ? significant : MA_NULL;
         },
     };
@@ -74,7 +74,7 @@ function deriveMa(block, rows, context) {
     if (pColumn.isErr())
         return err(pColumn.error);
     const composition = {
-        series: [{ form: "scatter", encoding: { x: x.value, y: y.value, ...(encoding.label !== undefined ? { label: encoding.label } : {}) } }],
+        series: [{ form: "scatter", encoding: { x: x.value, y: y.value, label: encoding.label } }],
         annotations: [{ kind: "reference-line", axis: "y", value: MA_BASELINE }],
         axes: { x: { scale: "log" } },
     };
@@ -90,7 +90,7 @@ function deriveMa(block, rows, context) {
     for (let index = 0; index < rows.length; index += 1) {
         const mean = xs[index];
         const effect = ys[index];
-        if (mean === null || effect === null || mean <= 0)
+        if (mean === null || mean === undefined || effect === null || effect === undefined || mean <= 0)
             continue;
         means.push(mean);
         effects.push(Math.abs(effect));
@@ -101,7 +101,11 @@ function deriveMa(block, rows, context) {
     const option = composed.value;
     return ok({
         ...option,
-        xAxis: { ...axisOf(option, "xAxis"), ...(low !== undefined && high !== undefined ? { min: decadeFloor(low), max: decadeCeiling(high) } : {}) },
+        xAxis: {
+            ...axisOf(option, "xAxis"),
+            min: low === undefined || high === undefined ? undefined : decadeFloor(low),
+            max: low === undefined || high === undefined ? undefined : decadeCeiling(high),
+        },
         yAxis: { ...axisOf(option, "yAxis"), ...symmetricRange(reach) },
         series: classification === undefined
             ? seriesOf(option).map((series) => ({ ...series, symbolSize: DENSE_SIGNAL_SYMBOL_PX }))

package/dist/report-render/figures/manhattan.d.ts

@@ -51,8 +51,7 @@ export declare function guideLabelBox(line: number, x: {
     readonly min: number;
     readonly max: number;
 }, top: number, text: string, frame: NameFrame): Box;
-/**
- * The genome order of two chromosome names: the numbered chromosomes in numeric order, then X, Y, and MT, then
+/** The genome order of two chromosome names: the numbered chromosomes in numeric order, then X, Y, and MT, then
  * each other name in text order. A `chr` prefix takes no part in the order.
  */
 export declare function compareChromosomes(a: Cell, b: Cell): number;

package/dist/report-render/figures/manhattan.js

@@ -27,12 +27,16 @@
  * as mark members, and the chromosome names and the lead names ride one series each after them. Thus the page
  * draws each of them over the payload points.
  */
+import { textOf } from "../../lib/unknown-text.js";
 import { err, ok } from "neverthrow";
 import { channelColumn } from "../../contracts/report-blocks.js";
 import { MANHATTAN_P_THRESHOLD } from "../chart-presets.js";
 import { GENOME_MEMBER, GENOME_POSITION_FUNCTION } from "../chart-toolbox.js";
+import { isUnknownArray } from "../../lib/unknown-array.js";
+import { parseUnknownRecord } from "../../lib/unknown-containers.js";
 import { CHART_INK, CHART_PALETTE, MUTED_CHART_COLOR } from "../design.js";
 import { formatNumberCell, typographicExponent } from "../number-format.js";
+import { isAllDigits } from "../../lib/text.js";
 import { categoryName, transformColumn } from "./common.js";
 import { axisOf, BELOW_RESOLUTION_NAME, BELOW_RESOLUTION_SYMBOL, BELOW_RESOLUTION_SYMBOL_PX, BELOW_RESOLUTION_TOOLTIP, belowResolutionHeight, belowResolutionRows, DENSE_NULL_SYMBOL_PX, DENSE_SIGNAL_OPACITY, demandedChannel, largest, niceCeiling, plottedValues, pointLayer, POINT_NAMES, pointNameSeries, seriesOf, sizedSeries, smallest, } from "./dense.js";
 import { placeLeaderNames, textWidthPx } from "./label-room.js";
@@ -141,28 +145,29 @@ function chromosomeNames(found) {
  */
 function genomeAxis(found) {
     const byPlace = [...found].sort((a, b) => a.low - b.low);
-    return {
-        names: CHROMOSOME_NAMES,
-        starts: byPlace.map((chromosome, index) => [
-            index === 0 ? 0 : byPlace[index - 1].high,
-            `chr${categoryName(chromosome.name).trim().replace(CHROMOSOME_PREFIX, "")}`,
-        ]),
-    };
+    const starts = [];
+    let previous;
+    for (const chromosome of byPlace) {
+        starts.push([previous === undefined ? 0 : previous.high, `chr${withoutChrPrefix(categoryName(chromosome.name).trim())}`]);
+        previous = chromosome;
+    }
+    return { names: CHROMOSOME_NAMES, starts };
 }
 /** The sides of a peak where a lead name sits, in the order that the figure tries them. */
 const LEAD_NAME_SIDES = ["top", "right", "left"];
 /** The place of the three named chromosomes after the numbered ones, in genome order. */
 const NAMED_CHROMOSOMES = { X: 0, Y: 1, MT: 2, M: 2 };
-/** The text prefix of a chromosome name that some tables carry, for example `chr1`. */
-const CHROMOSOME_PREFIX = /^chr/i;
-/**
- * The genome order of two chromosome names: the numbered chromosomes in numeric order, then X, Y, and MT, then
+/** The chromosome name without its leading `chr`, in either case. */
+function withoutChrPrefix(name) {
+    return name.toLowerCase().startsWith("chr") ? name.slice(3) : name;
+}
+/** The genome order of two chromosome names: the numbered chromosomes in numeric order, then X, Y, and MT, then
  * each other name in text order. A `chr` prefix takes no part in the order.
  */
 export function compareChromosomes(a, b) {
     const rank = (cell) => {
-        const name = String(cell).trim().replace(CHROMOSOME_PREFIX, "");
-        if (/^\d+$/.test(name))
+        const name = withoutChrPrefix(String(cell).trim());
+        if (name.length > 0 && isAllDigits(name))
             return [0, Number(name), name];
         const named = NAMED_CHROMOSOMES[name.toUpperCase()];
         return named !== undefined ? [1, named, name] : [2, 0, name];
@@ -184,10 +189,10 @@ function chromosomes(rows, groupColumn, labelColumn, xs, ys, line) {
     const byKey = new Map();
     const order = [];
     for (let index = 0; index < rows.length; index += 1) {
-        const value = rows[index][groupColumn];
+        const value = rows[index]?.[groupColumn];
         const x = xs[index];
         const y = ys[index];
-        if (value === undefined || x === null || y === null)
+        if (value === undefined || x === null || x === undefined || y === null || y === undefined)
             continue;
         // The key carries the type of the cell, as the series split does.
         const key = `${typeof value}:${String(value)}`;
@@ -199,7 +204,7 @@ function chromosomes(rows, groupColumn, labelColumn, xs, ys, line) {
         }
         chromosome.low = Math.min(chromosome.low, x);
         chromosome.high = Math.max(chromosome.high, x);
-        const name = labelColumn === undefined ? undefined : rows[index][labelColumn];
+        const name = labelColumn === undefined ? undefined : rows[index]?.[labelColumn];
         if (y > line && name !== undefined && String(name).trim() !== "" && (chromosome.lead === undefined || leads(index, chromosome.lead, xs, ys))) {
             chromosome.lead = index;
         }
@@ -217,12 +222,16 @@ function leads(index, other, xs, ys) {
 }
 /** The guide lines of a mark member, with the label of the genome-wide line over the line. */
 function guideOverLine(markLine, line) {
-    const data = Array.isArray(markLine.data) ? markLine.data : [];
+    const data = isUnknownArray(markLine.data) ? markLine.data : [];
     return {
         ...markLine,
-        data: data.map((entry) => entry.yAxis === line && typeof entry.label === "object" && entry.label !== null
-            ? { ...entry, label: { ...entry.label, position: GUIDE_OVER_LINE } }
-            : entry),
+        data: data.map((entry) => {
+            const fields = parseUnknownRecord(entry);
+            const label = fields === undefined ? undefined : parseUnknownRecord(fields.label);
+            if (fields === undefined || label === undefined || fields.yAxis !== line)
+                return entry;
+            return { ...fields, label: { ...label, position: GUIDE_OVER_LINE } };
+        }),
     };
 }
 /** The text of a guide p-value: the p in the scientific form of the number helper, as a power of ten. */
@@ -262,7 +271,7 @@ function deriveManhattan(block, rows, context) {
                     x: x.value,
                     y: { column: pColumn, transform: "neg_log10" },
                     group: group.value,
-                    ...(encoding.label !== undefined ? { label: encoding.label } : {}),
+                    label: encoding.label,
                 },
             },
         ],
@@ -284,12 +293,12 @@ function deriveManhattan(block, rows, context) {
     // The composition splits the series in the order of the rows, thus each series takes the color of the
     // genome place of its chromosome, and never of its place in the series list.
     const places = new Map(found.map((chromosome, place) => [categoryName(chromosome.name), place]));
-    const colorOf = (name) => MANHATTAN_COLORS[(places.get(String(name)) ?? 0) % MANHATTAN_COLORS.length];
+    const colorOf = (name) => MANHATTAN_COLORS[(places.get(textOf(name)) ?? 0) % MANHATTAN_COLORS.length] ?? CHART_PALETTE[0];
     const low = smallest(found.map((chromosome) => chromosome.low));
     const high = largest(found.map((chromosome) => chromosome.high));
     const top = niceCeiling(Math.max(peak, line, zeroRows.length > 0 ? zeroY : 0));
     const labelColumn = encoding.label;
-    const names = labelColumn === undefined ? [] : leadRows.map((index) => ({ x: xs[index] ?? 0, y: ys[index] ?? 0, text: String(rows[index][labelColumn]) }));
+    const names = labelColumn === undefined ? [] : leadRows.map((index) => ({ x: xs[index] ?? 0, y: ys[index] ?? 0, text: String(rows[index]?.[labelColumn]) }));
     const span = low !== undefined && high !== undefined ? { min: low, max: high } : undefined;
     const text = sizedSeries([CHROMOSOME_NAMES, POINT_NAMES], (frame) => {
         if (span === undefined)
@@ -306,18 +315,24 @@ function deriveManhattan(block, rows, context) {
         legend: { show: false },
         xAxis: {
             ...axisOf(option, "xAxis"),
-            ...(low !== undefined && high !== undefined ? { min: low, max: high } : {}),
+            min: low,
+            max: high,
             axisLabel: { show: false, formatter: GENOME_POSITION_FUNCTION },
             axisTick: { show: false },
             [GENOME_MEMBER]: genomeAxis(found),
         },
         yAxis: { ...axisOf(option, "yAxis"), min: 0, max: top },
         series: [
-            ...seriesOf(option).map((series) => ({
-                ...series,
-                ...pointLayer(colorOf(series.name), DENSE_NULL_SYMBOL_PX, DENSE_SIGNAL_OPACITY),
-                ...(series.markLine !== undefined ? { markLine: guideOverLine(series.markLine, line) } : {}),
-            })),
+            ...seriesOf(option).map((series) => {
+                const guided = {
+                    ...series,
+                    ...pointLayer(colorOf(series.name), DENSE_NULL_SYMBOL_PX, DENSE_SIGNAL_OPACITY),
+                };
+                if (series.markLine !== undefined) {
+                    guided.markLine = guideOverLine(parseUnknownRecord(series.markLine) ?? {}, line);
+                }
+                return guided;
+            }),
             ...(zeroRows.length > 0
                 ? [
                     {
@@ -327,11 +342,14 @@ function deriveManhattan(block, rows, context) {
                         symbolSize: BELOW_RESOLUTION_SYMBOL_PX,
                         itemStyle: { opacity: DENSE_SIGNAL_OPACITY },
                         tooltip: BELOW_RESOLUTION_TOOLTIP,
-                        data: zeroRows.map((index) => ({
-                            ...(labelColumn !== undefined ? { name: String(rows[index][labelColumn]) } : {}),
-                            value: [xs[index] ?? 0, zeroY],
-                            itemStyle: { color: colorOf(categoryName(rows[index][groupColumn])) },
-                        })),
+                        data: zeroRows.map((index) => {
+                            const group = rows[index]?.[groupColumn];
+                            return {
+                                name: labelColumn === undefined ? undefined : String(rows[index]?.[labelColumn]),
+                                value: [xs[index] ?? 0, zeroY],
+                                itemStyle: { color: group === undefined ? MANHATTAN_COLORS[0] : colorOf(categoryName(group)) },
+                            };
+                        }),
                     },
                 ]
                 : []),

package/dist/report-render/figures/oncoprint.js

@@ -173,11 +173,10 @@ function deriveOncoprint(block, rows, context) {
         legend: {
             // A taller body holds the legend lines of the single column export, thus the page legend starts
             // under the sample title and the free part of the band sits under it.
-            ...(tall
-                ? {
-                    top: percentOf(100 - bottom + ((CHART_PAGE_TEXT_PX * (1 + TITLE_LINE_SHARE) + SAMPLE_TITLE_GAP) / Math.min(body, CHART_BODY_MAX_PX)) * 100),
-                }
-                : { bottom: 0 }),
+            top: tall
+                ? percentOf(100 - bottom + ((CHART_PAGE_TEXT_PX * (1 + TITLE_LINE_SHARE) + SAMPLE_TITLE_GAP) / Math.min(body, CHART_BODY_MAX_PX)) * 100)
+                : undefined,
+            bottom: tall ? undefined : 0,
             itemWidth: LEGEND_ICON_PX,
             itemHeight: LEGEND_ICON_PX,
             itemGap: LEGEND_GAP_PX,

package/dist/report-render/figures/pca.js

@@ -17,6 +17,7 @@
  */
 import { err, ok } from "neverthrow";
 import { channelColumn, channelOrder, channelTransform } from "../../contracts/report-blocks.js";
+import { parseUnknownRecord } from "../../lib/unknown-containers.js";
 import { CHART_INK, CHART_PALETTE } from "../design.js";
 import { categoricalPalette, categoryName, chartProblem, columnPresent, firstAppearance, POINT_LEGEND_ICON, toNumber, transformColumn, valueAxis, valueAxisTitle, } from "./common.js";
 import { equalRanges, squareLayout } from "./equal-units.js";
@@ -147,7 +148,13 @@ function deriveShapeDraw(block, rows, context, draw) {
         const ps = shapes?.values[index] ?? null;
         if (px === null || py === null || (groups !== undefined && pg === null) || (shapes !== undefined && ps === null))
             continue;
-        points.push({ index, x: px, y: py, ...(pg !== null ? { group: categoryName(pg) } : {}), ...(ps !== null ? { shape: categoryName(ps) } : {}) });
+        points.push({
+            index,
+            x: px,
+            y: py,
+            group: pg === null ? undefined : categoryName(pg),
+            shape: ps === null ? undefined : categoryName(ps),
+        });
     }
     const groupNames = firstAppearance(points.flatMap((point) => (point.group === undefined ? [] : [point.group])));
     const shapeNames = firstAppearance(points.flatMap((point) => (point.shape === undefined ? [] : [point.shape])));
@@ -164,10 +171,13 @@ function deriveShapeDraw(block, rows, context, draw) {
     const named = labelColumn !== undefined;
     const labeled = named && draw.labelRows > 0 && points.length <= draw.labelRows;
     const sides = new Map();
-    if (labeled && labelColumn !== undefined) {
-        const placed = pointNameSides(points.map((point) => ({ x: point.x, y: point.y, text: String(rows[point.index][labelColumn] ?? "") })), ranges, SHAPED_POINT_PX);
-        for (const [place, point] of points.entries())
-            sides.set(point.index, placed[place]);
+    if (labelColumn !== undefined && labeled) {
+        const placed = pointNameSides(points.map((point) => ({ x: point.x, y: point.y, text: String(rows[point.index]?.[labelColumn] ?? "") })), ranges, SHAPED_POINT_PX);
+        for (const [place, point] of points.entries()) {
+            const side = placed[place];
+            if (side !== undefined)
+                sides.set(point.index, side);
+        }
     }
     const buckets = new Map();
     for (const point of points) {
@@ -189,17 +199,21 @@ function deriveShapeDraw(block, rows, context, draw) {
             series.push({
                 type: "scatter",
                 name: groupKey ?? shapeKey ?? yTitle,
-                ...(shapeKey !== undefined ? { symbol: SHAPE_SYMBOLS[shapePlace] } : {}),
+                symbol: shapeKey !== undefined ? SHAPE_SYMBOLS[shapePlace] : undefined,
                 symbolSize: SHAPED_POINT_PX,
                 itemStyle: { color: groupKey !== undefined ? palette[groupPlace] : CHART_PALETTE[0] },
-                ...(labeled ? POINT_LABEL_FIELDS : {}),
+                label: labeled ? POINT_LABEL_FIELDS.label : undefined,
                 data: members.map((point) => {
                     const pair = [point.x, point.y];
-                    const name = labelColumn === undefined ? undefined : rows[point.index][labelColumn];
+                    const name = labelColumn === undefined ? undefined : rows[point.index]?.[labelColumn];
                     if (name === undefined)
                         return pair;
                     const side = sides.get(point.index);
-                    return { value: pair, name: String(name), ...(side !== undefined && side !== "right" ? { label: { position: side } } : {}) };
+                    return {
+                        value: pair,
+                        name: String(name),
+                        label: side !== undefined && side !== "right" ? { position: side } : undefined,
+                    };
                 }),
             });
         }
@@ -219,7 +233,7 @@ function deriveShapeDraw(block, rows, context, draw) {
     const option = {
         tooltip: named ? { ...NAMED_POINT_TOOLTIP } : { ...PLAIN_POINT_TOOLTIP },
         series,
-        legend: keyed ? { orient: draw.equalUnits ? "vertical" : "horizontal", ...(draw.equalUnits ? {} : { bottom: 0 }), data: entries } : { show: false },
+        legend: keyed ? { orient: draw.equalUnits ? "vertical" : "horizontal", bottom: draw.equalUnits ? undefined : 0, data: entries } : { show: false },
     };
     if (!draw.equalUnits) {
         return ok({ ...option, xAxis: valueAxis("x", xTitle, { scale: true }), yAxis: valueAxis("y", yTitle, { scale: true }) });
@@ -231,7 +245,7 @@ function deriveShapeDraw(block, rows, context, draw) {
         grid: layout.grid,
         xAxis: { ...valueAxis("x", xTitle, ranges.x), ...interval },
         yAxis: { ...valueAxis("y", yTitle, ranges.y), ...interval },
-        ...(keyed && layout.legend !== undefined ? { legend: { ...option.legend, ...layout.legend } } : {}),
+        legend: { ...parseUnknownRecord(option.legend), ...layout.legend },
         media: layout.media,
     });
 }