react-cheminfo 0.9.0 → 0.11.0

package/lib/scatter/ui/scatterMatrixProps.d.ts

@@ -0,0 +1,99 @@
+/**
+ * What a caller hands a {@link ScatterMatrix}.
+ *
+ * The types live beside the component rather than inside it because the grid's
+ * own file would otherwise be mostly prose: a reader looking for what the
+ * component draws should not have to scroll past twenty documented options to
+ * find it.
+ */
+import type { ReactNode } from 'react';
+import type { MatrixLike } from '../../chart/core/matrix.ts';
+import type { EllipseSize } from '../core/confidenceEllipse.ts';
+import type { ScatterGroup } from './scatterPlotProps.ts';
+/** One axis of a {@link ScatterMatrix}. */
+export interface ScatterMatrixAxis {
+    /** What it is called, e.g. `PC 1`. */
+    name: string;
+    /**
+     * The share of the differences it accounts for, between 0 and 1.
+     * @default undefined — nothing is written after the name
+     */
+    share?: number;
+}
+/** What {@link ScatterMatrix} needs. */
+export interface ScatterMatrixProps {
+    /** The coordinates: one row per sample, one column per axis. */
+    scores: MatrixLike;
+    /** The axes, in order; only the first `count` are laid out. */
+    axes: readonly ScatterMatrixAxis[];
+    /**
+     * How many axes to lay out, up to six. Reduced on its own when the container
+     * is too narrow for readable cells, and the reduction is shown in the
+     * options rather than applied silently.
+     * @default the smaller of six and the number of axes
+     */
+    count?: number;
+    /** Available width, in pixels, from `useContainerSize`. */
+    width: number;
+    /**
+     * Which group each row belongs to, for the colours, for the outlines and for
+     * the strip along the diagonal.
+     * @default undefined — every row is drawn in one colour
+     */
+    groupOf?: ArrayLike<number>;
+    /**
+     * The groups, in the order they are coloured.
+     * @default undefined
+     */
+    groups?: readonly ScatterGroup[];
+    /**
+     * How large the outline drawn around each group in each cell is, or `null`
+     * for none. Nothing is outlined unless the groups are named.
+     * @default { kind: 'coverage', probability: 0.95 }
+     */
+    ellipse?: EllipseSize | null;
+    /**
+     * How many rows a group needs before it is outlined at all. Below it the
+     * shape says more about the sample than about the group.
+     * @default 3
+     */
+    ellipseMinimumPoints?: number;
+    /**
+     * The rows selected elsewhere; the rest are drawn faint.
+     * @default undefined — every row is drawn at full strength
+     */
+    selected?: readonly number[];
+    /**
+     * Called with the axis pair a cell stands for, so the map tab can take it
+     * over. A diagonal cell offers itself against its neighbour, which is what
+     * the reader meant by clicking it.
+     * @default undefined — the cells are not clickable
+     */
+    onSelectPair?: (xAxis: number, yAxis: number) => void;
+    /**
+     * Called with the row under the pointer, or `-1`.
+     * @default undefined
+     */
+    onHoverChange?: (index: number) => void;
+    /**
+     * How many bins the diagonal's distribution is cut into.
+     * @default 24
+     */
+    bins?: number;
+    /**
+     * Radius of a dot, in pixels.
+     * @default 2
+     */
+    pointRadius?: number;
+    /**
+     * What floats over the grid.
+     * @default undefined
+     */
+    overlay?: ReactNode;
+    /**
+     * Value of the `data-testid` attribute of the wrapper.
+     * @default undefined
+     */
+    testId?: string;
+}
+//# sourceMappingURL=scatterMatrixProps.d.ts.map

package/lib/scatter/ui/scatterMatrixProps.d.ts.map

@@ -0,0 +1 @@
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package/lib/scatter/ui/scatterMatrixProps.js

@@ -0,0 +1,10 @@
+/**
+ * What a caller hands a {@link ScatterMatrix}.
+ *
+ * The types live beside the component rather than inside it because the grid's
+ * own file would otherwise be mostly prose: a reader looking for what the
+ * component draws should not have to scroll past twenty documented options to
+ * find it.
+ */
+export {};
+//# sourceMappingURL=scatterMatrixProps.js.map

package/lib/scatter/ui/scatterMatrixProps.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"scatterMatrixProps.js","sourceRoot":"","sources":["../../../src/scatter/ui/scatterMatrixProps.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG"}

package/lib/scatter/ui/scatterOutlineShape.d.ts

@@ -0,0 +1,63 @@
+/**
+ * How one group outline is drawn, wherever it is drawn.
+ *
+ * The map and the pair grid measure their groups differently — the map over
+ * two columns of points, the grid over one shared block of covariances — but a
+ * reader moving between the two tabs has to see the same picture, so the one
+ * decision about fill and the collinear case lives here rather than once per
+ * figure.
+ */
+import type { ReactElement } from 'react';
+import type { ChartScale } from '../../chart/core/chartScale.ts';
+import type { ConfidenceEllipse } from '../core/confidenceEllipse.ts';
+/** How one outline is inked. */
+export interface ScatterOutlineInk {
+    /** The group's own colour, which the region is filled with. */
+    color: string;
+    /**
+     * How strongly the whole outline is drawn, which is what a muted legend
+     * entry turns down.
+     * @default undefined — the outline is drawn at full strength
+     */
+    opacity?: number;
+    /**
+     * How solid the region is; `0` draws nothing at all, since the fill is the
+     * whole shape.
+     * @default SCATTER_OUTLINE_FILL_OPACITY
+     */
+    fillOpacity?: number;
+}
+/**
+ * One group outline, mapped onto a plot and ready to be drawn.
+ *
+ * The region is fill only, with no boundary drawn: a stroked edge reads as a
+ * measured limit the ellipse never claims to be, and it competes with the dots
+ * the reader is there to count. The fill is deliberately faint for the same
+ * reason it is the whole shape — fills stack where groups overlap, and a tint
+ * heavy enough to see on its own turns two overlapping species into a third
+ * colour the reader then looks for in the legend.
+ *
+ * A group whose points lie on a straight line is drawn as the segment it
+ * actually is, and that one is stroked, since a shape of no height fills to
+ * nothing: that a group is perfectly correlated in these two axes is a
+ * finding, and dropping its outline would hide it.
+ * @param group - Which group it belongs to, for the key and the attribute the tests read.
+ * @param ellipse - The outline in data units, from `confidenceEllipse` or `scatterPairEllipse`.
+ * @param scaleX - Data to pixels, horizontally.
+ * @param scaleY - Data to pixels, vertically; its `factor` is negative.
+ * @param ink - See {@link ScatterOutlineInk}.
+ * @returns The element, keyed by group.
+ */
+export declare function scatterOutlineShape(group: number, ellipse: ConfidenceEllipse, scaleX: ChartScale, scaleY: ChartScale, ink: ScatterOutlineInk): ReactElement;
+/**
+ * How solid a group's region is.
+ *
+ * Three iris species overlap in the leading components, and fills compound
+ * where they do: at 0.2 two of them stack to 0.36 and read as a fourth group
+ * with a colour of its own, while at 0.1 they stack to 0.19 — denser than
+ * either, plainly still the same family. Below about 0.06 the region stops
+ * being visible against a white ground at all, which is the other failure.
+ * A caller drawing ten groups should turn it down.
+ */
+export declare const SCATTER_OUTLINE_FILL_OPACITY = 0.1;
+//# sourceMappingURL=scatterOutlineShape.d.ts.map

package/lib/scatter/ui/scatterOutlineShape.d.ts.map

@@ -0,0 +1 @@
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package/lib/scatter/ui/scatterOutlineShape.js

@@ -0,0 +1,82 @@
+import { jsx as _jsx } from "react/jsx-runtime";
+import { ellipsePolygon, projectEllipse } from "../core/ellipseProjection.js";
+/**
+ * One group outline, mapped onto a plot and ready to be drawn.
+ *
+ * The region is fill only, with no boundary drawn: a stroked edge reads as a
+ * measured limit the ellipse never claims to be, and it competes with the dots
+ * the reader is there to count. The fill is deliberately faint for the same
+ * reason it is the whole shape — fills stack where groups overlap, and a tint
+ * heavy enough to see on its own turns two overlapping species into a third
+ * colour the reader then looks for in the legend.
+ *
+ * A group whose points lie on a straight line is drawn as the segment it
+ * actually is, and that one is stroked, since a shape of no height fills to
+ * nothing: that a group is perfectly correlated in these two axes is a
+ * finding, and dropping its outline would hide it.
+ * @param group - Which group it belongs to, for the key and the attribute the tests read.
+ * @param ellipse - The outline in data units, from `confidenceEllipse` or `scatterPairEllipse`.
+ * @param scaleX - Data to pixels, horizontally.
+ * @param scaleY - Data to pixels, vertically; its `factor` is negative.
+ * @param ink - See {@link ScatterOutlineInk}.
+ * @returns The element, keyed by group.
+ */
+export function scatterOutlineShape(group, ellipse, scaleX, scaleY, ink) {
+    const drawn = projectEllipse(ellipse, scaleX, scaleY);
+    return drawn === null
+        ? sampledOutline(group, ellipse, scaleX, scaleY, ink)
+        : projectedOutline(group, drawn, ink);
+}
+/**
+ * How solid a group's region is.
+ *
+ * Three iris species overlap in the leading components, and fills compound
+ * where they do: at 0.2 two of them stack to 0.36 and read as a fourth group
+ * with a colour of its own, while at 0.1 they stack to 0.19 — denser than
+ * either, plainly still the same family. Below about 0.06 the region stops
+ * being visible against a white ground at all, which is the other failure.
+ * A caller drawing ten groups should turn it down.
+ */
+export const SCATTER_OUTLINE_FILL_OPACITY = 0.1;
+/** Firm enough to read over a cloud of its own colour. */
+const SEGMENT_STROKE_WIDTH = 1.5;
+const HALF_TURN_DEGREES = 180;
+function projectedOutline(group, shape, ink) {
+    const { cx, cy, rx, ry, angleDegrees } = shape;
+    const shared = { 'data-group': group, opacity: ink.opacity };
+    if (ry > 0) {
+        return (_jsx("ellipse", { ...shared, ...fillOf(ink), cx: round(cx), cy: round(cy), rx: round(rx), ry: round(ry), transform: `rotate(${round(angleDegrees)} ${round(cx)} ${round(cy)})` }, group));
+    }
+    const radians = (angleDegrees * Math.PI) / HALF_TURN_DEGREES;
+    const alongX = rx * Math.cos(radians);
+    const alongY = rx * Math.sin(radians);
+    return (_jsx("line", { ...shared, fill: "none", stroke: ink.color, strokeWidth: SEGMENT_STROKE_WIDTH, x1: round(cx - alongX), y1: round(cy - alongY), x2: round(cx + alongX), y2: round(cy + alongY) }, group));
+}
+/*
+ * The outline sampled and mapped point by point, for the one case the exact
+ * projection gives up on: coordinates large enough that squaring the mapping
+ * overflows. Mapping each point stays linear and so survives what squaring
+ * does not.
+ */
+function sampledOutline(group, ellipse, scaleX, scaleY, ink) {
+    const outline = ellipsePolygon(ellipse);
+    let path = '';
+    for (let index = 0; index < outline.length; index++) {
+        const point = outline[index];
+        if (point === undefined)
+            continue;
+        const px = round(scaleX.offset + point.x * scaleX.factor);
+        const py = round(scaleY.offset + point.y * scaleY.factor);
+        path += `${index === 0 ? 'M' : 'L'}${px} ${py}`;
+    }
+    return (_jsx("path", { "data-group": group, d: path === '' ? path : `${path}Z`, opacity: ink.opacity, ...fillOf(ink) }, group));
+}
+/* A fill of no opacity is left off the element rather than painted invisibly. */
+function fillOf(ink) {
+    const share = ink.fillOpacity ?? SCATTER_OUTLINE_FILL_OPACITY;
+    if (!(share > 0))
+        return { fill: 'none' };
+    return { fill: ink.color, fillOpacity: share };
+}
+const round = (value) => Math.round(value * 100) / 100;
+//# sourceMappingURL=scatterOutlineShape.js.map

package/lib/scatter/ui/scatterOutlineShape.js.map

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package/lib/scatter/ui/scatterPlotModel.d.ts

@@ -0,0 +1,107 @@
+/**
+ * What a scatter is made of before any of it is drawn: the groups it colours
+ * by, the marks laid over it, and the arithmetic that turns the caller's
+ * numbers into the pixels three layers and one hit test have to agree on.
+ *
+ * It is kept out of the component because a plot has to know its own rectangle
+ * before it can hand the interaction hook a set of screen positions, and a
+ * hook cannot be called from inside the frame's render callback.
+ */
+import type { ChartScale } from '../../chart/core/chartScale.ts';
+import type { ChartAxisSpec } from '../../chart/ui/ChartFrame.tsx';
+import type { ScreenPoints } from '../core/screenPoints.ts';
+import type { ScatterPixelMark } from './scatterMarkGlyph.tsx';
+import type { ScatterGroup, ScatterMarker } from './scatterPlotProps.ts';
+/** Where a scatter's data lands, and the rectangle it lands in. */
+export interface ScatterPlotView {
+    /** The rectangle gestures are taken on, ready to spread onto a `<rect>`. */
+    rect: {
+        x: number;
+        y: number;
+        width: number;
+        height: number;
+    };
+    /** Data to pixels, horizontally. */
+    toX: ChartScale;
+    /** Data to pixels, vertically; its `factor` is negative. */
+    toY: ChartScale;
+    /** Every point in the frame's pixels, the space a gesture arrives in. */
+    points: ScreenPoints;
+}
+/** The colour and the strength each group is drawn at. */
+export interface ScatterGroupInk {
+    /** One colour per group, in group order. */
+    colors: string[];
+    /** How strongly each group is drawn, in the same order. */
+    opacities: number[];
+}
+/**
+ * The plot rectangle, the two mappings, and every point in pixels.
+ *
+ * It repeats what `ChartFrame` works out for itself, from the same inputs and
+ * through the same two functions, because the interaction needs the positions
+ * before the frame has drawn anything and a hook cannot be called from inside
+ * the frame's render callback. Both answers come out of `chartPlotArea`, so
+ * they cannot drift apart without the frame's own tests saying so.
+ * @param x - Horizontal coordinate of every point, in data units.
+ * @param y - Vertical coordinate, in the same order.
+ * @param width - Total width of the figure, in pixels.
+ * @param height - Total height.
+ * @param xAxis - How the horizontal axis was asked for.
+ * @param yAxis - How the vertical one was.
+ * @returns Where everything sits.
+ */
+export declare function scatterPlotGeometry(x: ArrayLike<number>, y: ArrayLike<number>, width: number, height: number, xAxis: ChartAxisSpec, yAxis: ChartAxisSpec): ScatterPlotView;
+/**
+ * The colour of each group and how strongly it is drawn.
+ *
+ * A muted group is drawn faint rather than dropped: the reader turned it off
+ * to see past it, not to change the shape of what is left, and a cloud that
+ * loses points as entries are switched off is a cloud nobody can compare.
+ * @param groups - The groups, in the order they are coloured and listed.
+ * @param muted - The ids drawn faint.
+ * @returns One colour and one opacity per group.
+ */
+export declare function scatterGroupInk(groups: readonly ScatterGroup[] | undefined, muted: ReadonlySet<string> | undefined): ScatterGroupInk;
+/**
+ * The markers in pixels, which is the only space the layer that draws them
+ * knows about.
+ * @param markers - The marks, in data units.
+ * @param toX - Data to pixels, horizontally.
+ * @param toY - Data to pixels, vertically.
+ * @returns The same marks, placed.
+ */
+export declare function scatterPixelMarks(markers: readonly ScatterMarker[] | undefined, toX: ChartScale, toY: ChartScale): ScatterPixelMark[];
+/**
+ * What a screen reader is told when the caller says nothing.
+ *
+ * A figure with no label at all is hidden from a reader entirely, which for a
+ * plot carrying the whole result is worse than a sentence nobody wrote by
+ * hand. The axes are named the way the plot names them, so a reader hearing
+ * `PC 2 against PC 1` hears the same words a sighted reader sees.
+ * @param xAxis - The horizontal axis.
+ * @param yAxis - The vertical axis.
+ * @param count - How many points are drawn.
+ * @returns The sentence.
+ */
+export declare function scatterPlotLabel(xAxis: ChartAxisSpec, yAxis: ChartAxisSpec, count: number): string;
+/**
+ * The ring being dragged. Dashed, and filled only faintly: it is a gesture in
+ * progress and not anything the data says, and a solid shape over the cloud
+ * would hide the very points it is about to pick.
+ */
+export declare const LASSO_STYLE: {
+    readonly fill: "var(--accent)";
+    readonly fillOpacity: 0.08;
+    readonly stroke: "var(--accent)";
+    readonly strokeWidth: 1.5;
+    readonly strokeDasharray: "5 4";
+    readonly pointerEvents: "none";
+};
+/**
+ * How far past the dot itself the pointer still counts as aiming at it. A
+ * scatter is aimed at with a hand, and a three-pixel dot that answers only
+ * when the pointer is exactly on it reads as a plot with no hover at all.
+ */
+export declare const SCATTER_HOVER_SLACK = 8;
+//# sourceMappingURL=scatterPlotModel.d.ts.map

package/lib/scatter/ui/scatterPlotModel.d.ts.map

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package/lib/scatter/ui/scatterPlotModel.js

@@ -0,0 +1,139 @@
+/**
+ * What a scatter is made of before any of it is drawn: the groups it colours
+ * by, the marks laid over it, and the arithmetic that turns the caller's
+ * numbers into the pixels three layers and one hit test have to agree on.
+ *
+ * It is kept out of the component because a plot has to know its own rectangle
+ * before it can hand the interaction hook a set of screen positions, and a
+ * hook cannot be called from inside the frame's render callback.
+ */
+import { chartAxisScale } from "../../chart/core/chartAxisScale.js";
+import { chartScale } from "../../chart/core/chartScale.js";
+import { chartOuterRoom, chartPlotArea } from "../../chart/ui/chartStyles.js";
+/**
+ * The plot rectangle, the two mappings, and every point in pixels.
+ *
+ * It repeats what `ChartFrame` works out for itself, from the same inputs and
+ * through the same two functions, because the interaction needs the positions
+ * before the frame has drawn anything and a hook cannot be called from inside
+ * the frame's render callback. Both answers come out of `chartPlotArea`, so
+ * they cannot drift apart without the frame's own tests saying so.
+ * @param x - Horizontal coordinate of every point, in data units.
+ * @param y - Vertical coordinate, in the same order.
+ * @param width - Total width of the figure, in pixels.
+ * @param height - Total height.
+ * @param xAxis - How the horizontal axis was asked for.
+ * @param yAxis - How the vertical one was.
+ * @returns Where everything sits.
+ */
+export function scatterPlotGeometry(x, y, width, height, xAxis, yAxis) {
+    const across = chartAxisScale(xAxis.domain[0], xAxis.domain[1], {
+        count: xAxis.tickCount,
+        nice: xAxis.nice,
+    });
+    const up = chartAxisScale(yAxis.domain[0], yAxis.domain[1], {
+        count: yAxis.tickCount,
+        nice: yAxis.nice,
+    });
+    const plot = chartPlotArea(width, height, {}, {
+        bottom: chartOuterRoom('bottom', xAxis, across),
+        left: chartOuterRoom('left', yAxis, up),
+    });
+    const toX = chartScale(across.domain[0], across.domain[1], plot.left, plot.right);
+    const toY = chartScale(up.domain[0], up.domain[1], plot.bottom, plot.top);
+    const total = Math.min(x.length, y.length);
+    const pixelX = new Float64Array(total);
+    const pixelY = new Float64Array(total);
+    for (let index = 0; index < total; index++) {
+        pixelX[index] = toX.offset + (x[index] ?? Number.NaN) * toX.factor;
+        pixelY[index] = toY.offset + (y[index] ?? Number.NaN) * toY.factor;
+    }
+    return {
+        rect: { x: plot.left, y: plot.top, width: plot.width, height: plot.height },
+        toX,
+        toY,
+        points: { x: pixelX, y: pixelY },
+    };
+}
+/**
+ * The colour of each group and how strongly it is drawn.
+ *
+ * A muted group is drawn faint rather than dropped: the reader turned it off
+ * to see past it, not to change the shape of what is left, and a cloud that
+ * loses points as entries are switched off is a cloud nobody can compare.
+ * @param groups - The groups, in the order they are coloured and listed.
+ * @param muted - The ids drawn faint.
+ * @returns One colour and one opacity per group.
+ */
+export function scatterGroupInk(groups, muted) {
+    const colors = [];
+    const opacities = [];
+    for (const group of groups ?? []) {
+        colors.push(group.color);
+        opacities.push(muted?.has(group.id) === true ? MUTED_OPACITY : 1);
+    }
+    return { colors, opacities };
+}
+/**
+ * The markers in pixels, which is the only space the layer that draws them
+ * knows about.
+ * @param markers - The marks, in data units.
+ * @param toX - Data to pixels, horizontally.
+ * @param toY - Data to pixels, vertically.
+ * @returns The same marks, placed.
+ */
+export function scatterPixelMarks(markers, toX, toY) {
+    const marks = [];
+    for (const marker of markers ?? []) {
+        marks.push({
+            label: marker.label,
+            color: marker.color,
+            shape: marker.shape,
+            x: toX.offset + marker.x * toX.factor,
+            y: toY.offset + marker.y * toY.factor,
+        });
+    }
+    return marks;
+}
+/**
+ * What a screen reader is told when the caller says nothing.
+ *
+ * A figure with no label at all is hidden from a reader entirely, which for a
+ * plot carrying the whole result is worse than a sentence nobody wrote by
+ * hand. The axes are named the way the plot names them, so a reader hearing
+ * `PC 2 against PC 1` hears the same words a sighted reader sees.
+ * @param xAxis - The horizontal axis.
+ * @param yAxis - The vertical axis.
+ * @param count - How many points are drawn.
+ * @returns The sentence.
+ */
+export function scatterPlotLabel(xAxis, yAxis, count) {
+    const across = xAxis.label ?? 'the horizontal axis';
+    const up = yAxis.label ?? 'the vertical axis';
+    return `A scatter plot of ${count} points, ${up} against ${across}.`;
+}
+/**
+ * The ring being dragged. Dashed, and filled only faintly: it is a gesture in
+ * progress and not anything the data says, and a solid shape over the cloud
+ * would hide the very points it is about to pick.
+ */
+export const LASSO_STYLE = {
+    fill: 'var(--accent)',
+    fillOpacity: 0.08,
+    stroke: 'var(--accent)',
+    strokeWidth: 1.5,
+    strokeDasharray: '5 4',
+    pointerEvents: 'none',
+};
+/**
+ * How far past the dot itself the pointer still counts as aiming at it. A
+ * scatter is aimed at with a hand, and a three-pixel dot that answers only
+ * when the pointer is exactly on it reads as a plot with no hover at all.
+ */
+export const SCATTER_HOVER_SLACK = 8;
+/**
+ * Faint enough to read as switched off at a glance, dark enough that the shape
+ * of the group is still there — a reader mutes a group to see past it.
+ */
+const MUTED_OPACITY = 0.2;
+//# sourceMappingURL=scatterPlotModel.js.map

package/lib/scatter/ui/scatterPlotModel.js.map

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