react-cheminfo 0.9.0 → 0.10.0

package/lib/projection/core/projectionCopy.js.map

@@ -0,0 +1 @@
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package/lib/projection/core/projectionCopyPatch.d.ts

@@ -0,0 +1,13 @@
+/**
+ * Every property of an object made optional, all the way down.
+ *
+ * It exists for one thing: a site overriding a single sentence of a viewer's
+ * copy should not have to restate the other sixty. The name carries its
+ * domain because every export of this package shares one flat namespace, and
+ * a bare `DeepPartial` there is a collision waiting for the next domain that
+ * wants one.
+ */
+export type ProjectionCopyPatch<T> = {
+    [K in keyof T]?: T[K] extends object ? ProjectionCopyPatch<T[K]> : T[K];
+};
+//# sourceMappingURL=projectionCopyPatch.d.ts.map

package/lib/projection/core/projectionCopyPatch.d.ts.map

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package/lib/projection/core/projectionCopyPatch.js

@@ -0,0 +1,2 @@
+export {};
+//# sourceMappingURL=projectionCopyPatch.js.map

package/lib/projection/core/projectionCopyPatch.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"projectionCopyPatch.js","sourceRoot":"","sources":["../../../src/projection/core/projectionCopyPatch.ts"],"names":[],"mappings":""}

package/lib/projection/core/projectionOptions.d.ts

@@ -0,0 +1,131 @@
+import type { EllipseSize } from '../../scatter/core/confidenceEllipse.ts';
+import type { ScatterSelectionMode } from '../../scatter/core/scatterSelection.ts';
+import type { ProjectionResult } from './projectionResult.ts';
+/** What the "what differs" panels draw. */
+export type ProjectionVariablesView = 
+/** The average sample pushed to each end of the component, in the data's own units. */
+'effect'
+/** The weight the component gives each measurement, above or below zero. */
+ | 'weights'
+/** The same weights undone through the scaling, so tall peaks read as tall again. */
+ | 'rescaled'
+/** The one selected sample, rebuilt from the components shown. */
+ | 'sample';
+/**
+ * What decides a dot's colour on the map: `'group'`, `'none'`, or nothing else
+ * in this release.
+ */
+export type ProjectionColorBy = 'group' | 'none';
+/** What the figure is currently showing. Every field is a control in the floating bar. */
+export interface ProjectionOptions {
+    /**
+     * Which axis is drawn horizontally, from 0.
+     * @default 0
+     */
+    xAxis: number;
+    /**
+     * Which axis is drawn vertically.
+     * @default 1
+     */
+    yAxis: number;
+    /**
+     * What decides a dot's colour.
+     * @default 'group'
+     */
+    colorBy: ProjectionColorBy;
+    /**
+     * How large the group outlines are, or `null` for none.
+     * @default { kind: 'coverage', probability: 0.95 }
+     */
+    ellipse: EllipseSize | null;
+    /**
+     * Radius of a dot on the map, in pixels.
+     * @default 3.5
+     */
+    pointRadius: number;
+    /**
+     * Whether each group's average is marked with a cross.
+     * @default false
+     */
+    showGroupMeans: boolean;
+    /**
+     * Whether each group's name is written once, over the middle of that group.
+     * @default false
+     */
+    showGroupLabels: boolean;
+    /**
+     * Whether every sample's own name is written beside its dot.
+     * @default false
+     */
+    showIds: boolean;
+    /**
+     * How many axes the pair grid lays out.
+     * @default 4
+     */
+    pairCount: number;
+    /**
+     * What the "what differs" panels draw.
+     * @default 'effect'
+     */
+    variablesView: ProjectionVariablesView;
+    /**
+     * How many components those panels show. The later ones usually carry noise.
+     * @default 3
+     */
+    variablesCount: number;
+    /**
+     * Whether every panel is drawn on one vertical scale, so a weak component
+     * looks weak. Fitting each panel to itself makes a component carrying two
+     * per cent of the differences look as important as one carrying fifty.
+     * @default true
+     */
+    sharedScale: boolean;
+    /**
+     * Whether the average sample is drawn faintly behind each panel. Without it
+     * the reader cannot tell which peak a wiggle belongs to.
+     * @default true
+     */
+    showAverage: boolean;
+    /**
+     * How far along a component the average sample is pushed, in standard
+     * deviations of that component's scores.
+     * @default 2
+     */
+    spread: number;
+    /**
+     * Order of the bars when the measurements are named. `original` keeps a
+     * measurement in the same slot in every panel, so the panels can be read
+     * down a column.
+     * @default 'original'
+     */
+    variableOrder: 'original' | 'strongest';
+    /**
+     * The cumulative share the marker on the shares tab aims at; `0` draws none.
+     * @default 0.95
+     */
+    shareTarget: number;
+    /**
+     * What a drag does to the selection when no modifier is held.
+     * @default 'replace'
+     */
+    selectMode: ScatterSelectionMode;
+}
+/** Every option, by name, so the help cannot drift from the controls. */
+export type ProjectionOptionId = keyof ProjectionOptions;
+/** What the figure shows when a site overrides nothing. */
+export declare const DEFAULT_PROJECTION_OPTIONS: ProjectionOptions;
+/**
+ * The options the viewer will use, with a caller's overrides merged in and
+ * every one of them made safe against the result that actually came back.
+ *
+ * A saved option outlives the data it was made on: reload with fewer samples
+ * and axis eight no longer exists. Rather than let a plot ask for a column
+ * that is not there, the two axes are pulled back inside what was computed and
+ * kept apart, the counts are held inside what exists, and a view whose data is
+ * missing falls back to `weights`.
+ * @param overrides - What the caller asked for.
+ * @param result - The reduced space the options will be applied to.
+ * @returns Every option, complete and safe.
+ */
+export declare function resolveProjectionOptions(overrides: Partial<ProjectionOptions> | undefined, result: ProjectionResult): ProjectionOptions;
+//# sourceMappingURL=projectionOptions.d.ts.map

package/lib/projection/core/projectionOptions.d.ts.map

@@ -0,0 +1 @@
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package/lib/projection/core/projectionOptions.js

@@ -0,0 +1,85 @@
+import { drawableVariablesView } from "./variablesView.js";
+/** What the figure shows when a site overrides nothing. */
+export const DEFAULT_PROJECTION_OPTIONS = {
+    xAxis: 0,
+    yAxis: 1,
+    colorBy: 'group',
+    ellipse: { kind: 'coverage', probability: 0.95 },
+    pointRadius: 3.5,
+    showGroupMeans: false,
+    showGroupLabels: false,
+    showIds: false,
+    pairCount: 4,
+    variablesView: 'effect',
+    variablesCount: 3,
+    sharedScale: true,
+    showAverage: true,
+    spread: 2,
+    variableOrder: 'original',
+    shareTarget: 0.95,
+    selectMode: 'replace',
+};
+const SMALLEST_PAIR_GRID = 2;
+const SMALLEST_PANEL_COUNT = 1;
+/**
+ * The options the viewer will use, with a caller's overrides merged in and
+ * every one of them made safe against the result that actually came back.
+ *
+ * A saved option outlives the data it was made on: reload with fewer samples
+ * and axis eight no longer exists. Rather than let a plot ask for a column
+ * that is not there, the two axes are pulled back inside what was computed and
+ * kept apart, the counts are held inside what exists, and a view whose data is
+ * missing falls back to `weights`.
+ * @param overrides - What the caller asked for.
+ * @param result - The reduced space the options will be applied to.
+ * @returns Every option, complete and safe.
+ */
+export function resolveProjectionOptions(overrides, result) {
+    const axisCount = result.axes.length;
+    const lastAxis = Math.max(0, axisCount - 1);
+    const xAxis = clampIndex(pick(overrides, 'xAxis'), lastAxis);
+    return {
+        xAxis,
+        yAxis: apart(clampIndex(pick(overrides, 'yAxis'), lastAxis), xAxis, lastAxis),
+        colorBy: pick(overrides, 'colorBy'),
+        ellipse: pick(overrides, 'ellipse'),
+        pointRadius: atLeast(pick(overrides, 'pointRadius'), 3.5, 0),
+        showGroupMeans: pick(overrides, 'showGroupMeans'),
+        showGroupLabels: pick(overrides, 'showGroupLabels'),
+        showIds: pick(overrides, 'showIds'),
+        pairCount: clampCount(pick(overrides, 'pairCount'), DEFAULT_PROJECTION_OPTIONS.pairCount, SMALLEST_PAIR_GRID, Math.max(SMALLEST_PAIR_GRID, axisCount)),
+        variablesView: drawableVariablesView(pick(overrides, 'variablesView'), result.loadings),
+        variablesCount: clampCount(pick(overrides, 'variablesCount'), DEFAULT_PROJECTION_OPTIONS.variablesCount, SMALLEST_PANEL_COUNT, Math.max(SMALLEST_PANEL_COUNT, axisCount)),
+        sharedScale: pick(overrides, 'sharedScale'),
+        showAverage: pick(overrides, 'showAverage'),
+        spread: atLeast(pick(overrides, 'spread'), 2, 0),
+        variableOrder: pick(overrides, 'variableOrder'),
+        shareTarget: Math.min(1, atLeast(pick(overrides, 'shareTarget'), 0.95, 0)),
+        selectMode: pick(overrides, 'selectMode'),
+    };
+}
+function pick(overrides, key) {
+    // Only an absent override defers to the default: `ellipse: null` is a
+    // reader who turned the outlines off, not a reader who said nothing.
+    const value = overrides?.[key];
+    return value === undefined ? DEFAULT_PROJECTION_OPTIONS[key] : value;
+}
+function clampIndex(value, lastAxis) {
+    if (!Number.isFinite(value))
+        return 0;
+    return Math.min(lastAxis, Math.max(0, Math.floor(value)));
+}
+function apart(yAxis, xAxis, lastAxis) {
+    if (yAxis !== xAxis)
+        return yAxis;
+    // One axis against itself is a diagonal line, which says nothing at all.
+    return xAxis > 0 ? xAxis - 1 : Math.min(1, lastAxis);
+}
+function clampCount(value, fallback, lowest, highest) {
+    const wanted = Number.isFinite(value) ? Math.floor(value) : fallback;
+    return Math.min(highest, Math.max(lowest, wanted));
+}
+function atLeast(value, fallback, floor) {
+    return Math.max(floor, Number.isFinite(value) ? value : fallback);
+}
+//# sourceMappingURL=projectionOptions.js.map

package/lib/projection/core/projectionOptions.js.map

@@ -0,0 +1 @@
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package/lib/projection/core/projectionResult.d.ts

@@ -0,0 +1,119 @@
+import type { MatrixLike } from '../../chart/core/matrix.ts';
+import type { OverlayMarkShape } from '../../overlay/core/overlayMarks.ts';
+import type { VariableAxis } from './variableAxis.ts';
+/** One axis of a reduced space — a component, a UMAP dimension. */
+export interface ProjectionAxis {
+    /** What it is called on an axis: `PC 1`, `UMAP 1`. */
+    name: string;
+    /**
+     * The share of the differences between the samples it accounts for, between
+     * 0 and 1 — a fraction, never a percentage. Left out by a method that
+     * publishes no such number, which is what removes the "how much each
+     * explains" tab rather than showing it empty.
+     * @default undefined
+     */
+    share?: number;
+    /**
+     * The variance of this axis' own scores, shown only in the fine print of a
+     * hover card, for the one reader in fifty who wants it.
+     * @default undefined
+     */
+    eigenvalue?: number;
+}
+/** A reference point drawn over the map that is not a sample. */
+export interface ProjectionMarker {
+    /** What it is called, e.g. `Centre of cluster 2`. */
+    label: string;
+    /** Its position, one value per axis, in the embedding's own units. */
+    position: readonly number[];
+    /**
+     * Which group it belongs to, as an index into the resolved groups, so it
+     * takes that group's colour.
+     * @default -1 — it is drawn in the muted ink
+     */
+    group?: number;
+    /**
+     * The glyph it is drawn with.
+     * @default 'cross'
+     */
+    shape?: OverlayMarkShape;
+}
+/** What each original measurement contributes to each axis. */
+export interface ProjectionLoadings {
+    /**
+     * The weight of every measurement in every axis: row `i` is axis `i`,
+     * column `j` is original measurement `j` — the orientation `ml-pca`'s
+     * `getLoadings()` returns.
+     */
+    weights: MatrixLike;
+    /** How the measurements are laid out, which decides a line or bars. */
+    variables: VariableAxis;
+    /**
+     * The average of every measurement, in the data's own units. Without it the
+     * panel can only draw weights; with it, it can draw what a sample at each
+     * end of an axis actually looks like, which is the only view a reader who
+     * has never met a loading can read.
+     * @default undefined — the "effect on a sample" view is not offered
+     */
+    mean?: readonly number[];
+    /**
+     * The standard deviation of each axis' own scores, which is how far along an
+     * axis the average sample is pushed.
+     * @default undefined — the "effect on a sample" view is not offered
+     */
+    spread?: readonly number[];
+    /**
+     * The standard deviation of every measurement, when the model divided by it.
+     * Left out when it did not, which is what removes the "in your units" view,
+     * because it would then be the same drawing twice.
+     * @default undefined
+     */
+    scales?: readonly number[];
+    /**
+     * What the measured values are, for the vertical axis, e.g. `Absorbance`.
+     * @default '' — the axis carries no title
+     */
+    valueLabel?: string;
+}
+/** What a dimension-reduction run produced, whatever produced it. */
+export interface ProjectionResult {
+    /**
+     * What produced it, for the headings — `Principal components`, `UMAP`,
+     * `Clusters`. It is a display string and nothing in the viewer ever branches
+     * on it.
+     */
+    method: string;
+    /** The axes, in the order the score columns hold them. */
+    axes: readonly ProjectionAxis[];
+    /** Where every sample landed: one row per sample, one column per axis. */
+    scores: MatrixLike;
+    /**
+     * What loads onto each axis. Left out by a method that cannot say — UMAP and
+     * t-SNE cannot — which is what removes the "what differs" tab.
+     * @default undefined
+     */
+    loadings?: ProjectionLoadings;
+    /**
+     * Reference points drawn over the map: the centres of a k-means run.
+     * @default undefined
+     */
+    markers?: readonly ProjectionMarker[];
+    /**
+     * How many leading rows the model was built from, the rest having been
+     * placed into it afterwards.
+     *
+     * The distinction is worth drawing because the two kinds of row are not
+     * equally trustworthy: a sample the model was fitted on helped choose where
+     * the axes point, so it is bound to sit somewhere reasonable, while one
+     * projected later can land anywhere — and landing far out is the finding,
+     * not a fault. The map draws the fitted samples filled and the projected
+     * ones hollow, and says so in its legend.
+     *
+     * Rows must therefore be ordered fitted-first, which is the order both
+     * `pcaResult` and a `getEmbedding()` followed by a `transform()` already
+     * produce.
+     * @default undefined — every row built the model
+     */
+    fittedCount?: number;
+}
+//# sourceMappingURL=projectionResult.d.ts.map

package/lib/projection/core/projectionResult.d.ts.map

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package/lib/projection/core/projectionResult.js

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+export {};
+//# sourceMappingURL=projectionResult.js.map

package/lib/projection/core/projectionResult.js.map

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package/lib/projection/core/projectionSamples.d.ts

@@ -0,0 +1,77 @@
+/** One line of the card that appears when the pointer rests on a sample. */
+export interface ProjectionField {
+    /** What the value is. */
+    label: string;
+    /** The value, already written out. */
+    value: string;
+}
+/** Who the rows are: what they are called, what they belong to, what is known. */
+export interface ProjectionSamples {
+    /**
+     * A stable name per row, in the score matrix's row order. It is the currency
+     * of the selection callbacks, so a caller never has to keep a second index.
+     */
+    ids: readonly string[];
+    /**
+     * What each row belongs to — a species, a batch, a cluster. A row with no
+     * group is drawn in the muted ink and left out of every outline.
+     * @default undefined — every row is one crowd
+     */
+    groups?: ReadonlyArray<string | undefined>;
+    /**
+     * The order the groups are listed and coloured in.
+     * @default the order the groups first appear in `groups`
+     */
+    groupOrder?: readonly string[];
+    /**
+     * What the set of groups is called, for the legend's heading and the hover
+     * card — `Species`, `Cluster`, `Batch`.
+     * @default 'Group'
+     */
+    groupLabel?: string;
+    /**
+     * A colour per group. Anything not named here takes the next unused colour
+     * of the shared palette, so two groups never share one.
+     * @default undefined — every group is coloured from the palette
+     */
+    groupColors?: Readonly<Record<string, string>>;
+    /**
+     * Everything else worth showing about one row. A callback rather than an
+     * array, so a table of ten thousand rows builds one record when a reader
+     * points at one row, and none otherwise.
+     * @default undefined — the card shows the id, the group and the two axes
+     */
+    fields?: (index: number) => readonly ProjectionField[];
+}
+/** The groups as the viewer draws them, resolved once per change. */
+export interface ResolvedProjectionGroups {
+    /** What the set of groups is called. */
+    label: string;
+    /** The groups, in the order they are listed and coloured. */
+    entries: ReadonlyArray<{
+        /** The group's own name, which is also its id. */
+        id: string;
+        /** What it is called; the same as `id` today, kept apart for a future translation. */
+        label: string;
+        /** Its colour. */
+        color: string;
+        /** How many rows are in it. */
+        count: number;
+    }>;
+    /** Which group each row is in, as an index into `entries`, or `-1`. */
+    groupOf: Int32Array;
+}
+/**
+ * The groups a set of samples has, in a shape a legend and a plot can both
+ * read.
+ *
+ * A group named in `groupOrder` but held by no row is kept, so a legend does
+ * not reshuffle when a filter empties one; a row naming a group that is not in
+ * `groupOrder` is appended in the order it appears.
+ * @param samples - Who the rows are.
+ * @param count - How many rows there are, which is the score matrix's height.
+ * @returns The resolved groups. A set of samples with no `groups` gives no
+ * entries at all, and every row lands at `-1`.
+ */
+export declare function resolveProjectionGroups(samples: ProjectionSamples, count: number): ResolvedProjectionGroups;
+//# sourceMappingURL=projectionSamples.d.ts.map

package/lib/projection/core/projectionSamples.d.ts.map

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package/lib/projection/core/projectionSamples.js

@@ -0,0 +1,81 @@
+import { CHART_SERIES_COLORS, chartSeriesColor, } from "../../chart/core/chartPalette.js";
+const NO_GROUP = -1;
+const DEFAULT_GROUP_LABEL = 'Group';
+/**
+ * The groups a set of samples has, in a shape a legend and a plot can both
+ * read.
+ *
+ * A group named in `groupOrder` but held by no row is kept, so a legend does
+ * not reshuffle when a filter empties one; a row naming a group that is not in
+ * `groupOrder` is appended in the order it appears.
+ * @param samples - Who the rows are.
+ * @param count - How many rows there are, which is the score matrix's height.
+ * @returns The resolved groups. A set of samples with no `groups` gives no
+ * entries at all, and every row lands at `-1`.
+ */
+export function resolveProjectionGroups(samples, count) {
+    const rowCount = Number.isFinite(count) ? Math.max(0, Math.floor(count)) : 0;
+    const label = samples.groupLabel ?? DEFAULT_GROUP_LABEL;
+    const groupOf = new Int32Array(rowCount).fill(NO_GROUP);
+    const { groups, groupColors, groupOrder } = samples;
+    if (groups === undefined)
+        return { label, entries: [], groupOf };
+    const entries = [];
+    const indexOfGroup = new Map();
+    if (groupOrder !== undefined) {
+        for (const id of groupOrder)
+            appendGroup(entries, indexOfGroup, id);
+    }
+    for (let row = 0; row < rowCount; row++) {
+        const id = groups[row];
+        if (id === undefined)
+            continue;
+        const at = appendGroup(entries, indexOfGroup, id);
+        groupOf[row] = at;
+        const entry = entries[at];
+        if (entry !== undefined)
+            entry.count++;
+    }
+    paintGroups(entries, groupColors);
+    return { label, entries, groupOf };
+}
+function appendGroup(entries, indexOfGroup, id) {
+    const known = indexOfGroup.get(id);
+    if (known !== undefined)
+        return known;
+    const at = entries.length;
+    indexOfGroup.set(id, at);
+    entries.push({ id, label: id, color: '', count: 0 });
+    return at;
+}
+function paintGroups(entries, pinned) {
+    // Every pinned colour is taken out of the palette before any group draws
+    // from it, so pinning the third group's hue onto the first does not leave
+    // two groups wearing it.
+    const taken = new Set();
+    if (pinned !== undefined) {
+        for (const entry of entries) {
+            const color = pinned[entry.id];
+            if (color !== undefined)
+                taken.add(color.toLowerCase());
+        }
+    }
+    let cursor = 0;
+    for (const entry of entries) {
+        const own = pinned?.[entry.id];
+        if (own !== undefined) {
+            entry.color = own;
+            continue;
+        }
+        let color = chartSeriesColor(cursor, 'group');
+        while (cursor < CHART_SERIES_COLORS.length &&
+            taken.has(color.toLowerCase())) {
+            cursor++;
+            color = chartSeriesColor(cursor, 'group');
+        }
+        cursor++;
+        taken.add(color.toLowerCase());
+        entry.color = color;
+    }
+}
+//# sourceMappingURL=projectionSamples.js.map

package/lib/projection/core/projectionSamples.js.map

@@ -0,0 +1 @@
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