@genome-spy/core 0.36.1 → 0.37.1

package/dist/src/spec/transform.d.ts

@@ -0,0 +1,504 @@
+/**
+ * The name of the field or a JavaScript expression for accessing nested properties.
+ * Dots and brackets in the field name must be escaped.
+ */
+export type Field = string;
+
+export interface TransformParamsBase {
+    /** The type of the transform to be applied */
+    type: string;
+}
+
+export interface IdentifierParams extends TransformParamsBase {
+    type: "identifier";
+
+    /**
+     * **Default:** `"_uniqueId"`
+     */
+    as?: string;
+}
+export interface FilterParams extends TransformParamsBase {
+    type: "filter";
+
+    /** An expression string. The data object is removed if the expression evaluates to false. */
+    expr: string;
+}
+
+export interface FormulaParams extends TransformParamsBase {
+    type: "formula";
+
+    /** An expression string */
+    expr: string;
+
+    /** The (new) field where the computed value is written to */
+    as: string;
+}
+
+export interface ProjectParams extends TransformParamsBase {
+    type: "project";
+
+    /**
+     * The fields to be projected.
+     */
+    fields: Field[];
+
+    /**
+     * New names for the projected fields. If omitted, the names of the source fields are used.
+     */
+    as?: string[];
+}
+
+export interface RegexExtractParams extends TransformParamsBase {
+    type: "regexExtract";
+
+    /**
+     * A valid JavaScript regular expression with at least one group. For example: `"^Sample(\\d+)$"`.
+     *
+     * Read more at: https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expressions
+     **/
+    regex: string;
+
+    /**
+     * The source field
+     */
+    field: Field;
+
+    /**
+     * The new field or an array of fields where the extracted values are written.
+     */
+    as: string | string[];
+
+    /**
+     * Do not complain about invalid input. Just skip it and leave the new fields undefined on the affected datum.
+     *
+     * **Default:** `false`
+     **/
+    skipInvalidInput?: boolean;
+}
+
+export interface RegexFoldParams extends TransformParamsBase {
+    type: "regexFold";
+
+    /**
+     * A regular expression that matches to column names. The regex must have one
+     * capturing group that is used for extracting the key (e.g., a sample id)
+     * from the column name.
+     */
+    columnRegex: string[] | string;
+
+    /**
+     * A new column name for the extracted values.
+     */
+    asValue: string[] | string;
+
+    /**
+     * An optional regex that matches to fields that should not be included
+     * in the new folded data objects.
+     */
+    skipRegex?: string;
+
+    /**
+     * **Default:** `"sample"`
+     */
+    asKey?: string;
+}
+
+export type SortOrder = "ascending" | "descending";
+
+export interface CompareParams {
+    /**
+     * The field(s) to sort by
+     */
+    field: Field[] | Field;
+
+    /**
+     * The order(s) to use: `"ascending"` (default), `"descending"`.
+     */
+    order?: SortOrder[] | SortOrder;
+}
+
+export interface StackParams extends TransformParamsBase {
+    type: "stack";
+
+    /**
+     * The field to stack. If no field is defined, a constant value of one is assumed.
+     */
+    field?: Field;
+
+    /**
+     * The fields to be used for forming groups for different stacks.
+     */
+    groupby: Field[];
+
+    /**
+     * The sort order of data in each stack.
+     */
+    sort?: CompareParams;
+
+    /**
+     * How to offset the values in a stack.
+     * `"zero"` (default) starts stacking at 0.
+     * `"center"` centers the values around zero.
+     * `"normalize"` computes intra-stack percentages and normalizes the values to the range of `[0, 1]`.
+     * `"information"` computes a layout for a sequence logo. The total height of the stack reflects
+     * the group's information content.
+     */
+    offset?: "zero" | "center" | "normalize" | "information";
+
+    /**
+     * Fields to write the stacked values.
+     *
+     * **Default:** `["y0", "y1"]`
+     */
+    as: string[];
+
+    /**
+     * Cardinality, e.g., the number if distinct bases or amino acids. Used for
+     * information content calculation when the offset is `"information"`.
+     *
+     * **Default:** `4`
+     */
+    cardinality?: number;
+
+    /**
+     * The field that contains the base or amino acid. Used for
+     * information content calculation when the offset is `"information"`.
+     * The data objects that have `null` in the baseField are considered gaps
+     * and they are taken into account when scaling the the locus' information
+     * content.
+     */
+    baseField?: Field;
+}
+
+export interface AggregateParams extends TransformParamsBase {
+    type: "aggregate";
+
+    /**
+     * Which fields to use for grouping. Missing `groupby` results in a single
+     * group that includes all the data items.
+     */
+    groupby?: Field[];
+}
+
+export interface FlattenParams extends TransformParamsBase {
+    type: "flatten";
+
+    /**
+     * The field(s) to flatten. If no field is defined, the data object itself
+     * is treated as an array to be flattened.
+     */
+    fields?: Field[] | Field;
+
+    /**
+     * The output field name for the zero-based index of the array values. If unspecified, an index field is not added.
+     */
+    index?: string;
+
+    /**
+     * The output field name(s) for the flattened field.
+     *
+     * **Default:** the input fields.
+     */
+    as?: string[] | string;
+}
+
+export interface FlattenDelimitedParams extends TransformParamsBase {
+    type: "flattenDelimited";
+
+    /**
+     * The field(s) to split and flatten
+     */
+    // TODO: Rename to prular to make it consistent with the other flatten transforms
+    field: Field[] | Field;
+
+    /**
+     * Separator(s) used on the field(s)
+     * TODO: Rename to delimiter
+     */
+    separator: string[] | string;
+
+    /**
+     * The output field name(s) for the flattened field.
+     *
+     * **Default:** the input fields.
+     */
+    as?: string[] | string;
+}
+
+export interface FlattenSequenceParams extends TransformParamsBase {
+    type: "flattenSequence";
+
+    /**
+     * The field to flatten.
+     *
+     * **Default:** `"sequence"`
+     */
+    field?: Field;
+
+    /**
+     * Name of the fields where the zero-based index number and flattened
+     * sequence letter are written to.
+     *
+     * **Default:** `["pos", "sequence"]`
+     */
+    // TODO: Introduce "index" property to make it consistent with the other flatten transforms
+    as?: [string, string];
+}
+
+export interface PileupParams extends TransformParamsBase {
+    type: "pileup";
+
+    /**
+     * The field representing the start coordinate of the segment (inclusive).
+     */
+    start: Field;
+
+    /**
+     * The field representing the end coordinate of the segment (exclusive).
+     */
+    end: Field;
+
+    /**
+     * The output field name for the computed lane.
+     *
+     * **Default:** `"lane"`.
+     */
+    as?: string;
+
+    /**
+     * The spacing between adjacent segments on the same lane in coordinate units.
+     *
+     * **Default:** `1`.
+     */
+    spacing?: number;
+
+    /**
+     * An optional field indicating the preferred lane. Use together with the
+     * `preferredOrder` property.
+     */
+    preference?: Field;
+
+    /**
+     * The order of the lane preferences. The first element contains the value that
+     * should place the segment on the first lane and so forth.
+     * If the preferred lane is occupied, the first available lane is taken.
+     */
+    preferredOrder?: string[] | number[] | boolean[];
+}
+
+export interface CoverageParams extends TransformParamsBase {
+    type: "coverage";
+
+    /**
+     * An optional chromosome field that is passed through. TODO: groupby
+     */
+    chrom?: Field;
+
+    /**
+     * The field representing the start coordinate of the segment (inclusive).
+     */
+    start: Field;
+
+    /**
+     * The field representing the end coordinate of the segment (exclusive).
+     */
+    end: Field;
+
+    /**
+     * A field representing an optional weight for the segment. Can be used with
+     * copy ratios, for example.
+     */
+    weight?: Field;
+
+    /**
+     * The output field for the computed coverage.
+     */
+    as?: string;
+
+    /**
+     * The output field for the chromosome.
+     *
+     * **Default:** Same as `chrom`
+     */
+    asChrom?: string;
+
+    /**
+     * The output field for the start coordinate.
+     *
+     * **Default:** Same as `start`
+     */
+    asStart?: string;
+
+    /**
+     * The output field for the end coordinate.
+     *
+     * **Default:** Same as `end`
+     */
+    asEnd?: string;
+}
+
+export interface CollectParams extends TransformParamsBase {
+    type: "collect";
+
+    /**
+     * Arranges the data into consecutive batches based on the groups.
+     * This is mainly intended for internal use so that faceted data can
+     * be handled as batches.
+     */
+    groupby?: Field[];
+
+    /**
+     * The sort order.
+     */
+    sort?: CompareParams;
+}
+
+export interface SampleParams extends TransformParamsBase {
+    type: "sample";
+
+    /**
+     * The maximum sample size.
+     *
+     * **Default:** `500`
+     */
+    size?: number;
+}
+
+export interface MeasureTextParams extends TransformParamsBase {
+    type: "measureText";
+
+    field: Field;
+
+    fontSize: number;
+
+    as: string;
+
+    // TODO: FontFamily etc
+}
+
+export interface MergeFacetsParams extends TransformParamsBase {
+    type: "mergeFacets";
+}
+
+export interface LinearizeGenomicCoordinateParams extends TransformParamsBase {
+    type: "linearizeGenomicCoordinate";
+
+    /**
+     * Get the genome assembly from the scale of the channel.
+     *
+     * **Default:** `"x"`
+     */
+    channel?: "x" | "y";
+
+    /**
+     * The chromosome/contig field
+     */
+    chrom: Field;
+
+    /**
+     * The field or fields that contain intra-chromosomal positions
+     */
+    pos: Field | Field[];
+
+    /**
+     * An offset or offsets that allow for adjusting the numbering base. The offset
+     * is subtracted from the positions.
+     *
+     * GenomeSpy uses internally zero-based indexing with half-open intervals.
+     * UCSC-based formats (BED, etc.) generally use this scheme. However, for example,
+     * VCF files use one-based indexing and must be adjusted by setting the offset to
+     * `1`.
+     *
+     * **Default:** `0`
+     */
+    offset?: number | number[];
+
+    /**
+     * The output field or fields for linearized coordinates.
+     */
+    as: string | string[];
+}
+
+export interface FilterScoredLabelsParams extends TransformParamsBase {
+    type: "filterScoredLabels";
+
+    /**
+     * The field representing the score used for prioritization.
+     */
+    score: Field;
+
+    /**
+     * The field representing element's width in pixels
+     */
+    width: Field;
+
+    /**
+     * The field representing element's position on the domain.
+     */
+    pos: Field;
+
+    /**
+     * An optional field representing element's lane, e.g., if transcripts
+     * are shown using a piled up layout.
+     */
+    lane?: Field;
+
+    /**
+     * Padding (in pixels) around the element.
+     *
+     * **Default:** `0`
+     */
+    padding?: number;
+
+    /**
+     * **Default:** `"x"`
+     */
+    channel?: "x" | "y";
+}
+
+export interface FlattenCompressedExonsParams extends TransformParamsBase {
+    type: "flattenCompressedExons";
+
+    /**
+     * The field containing the exons.
+     *
+     * **Default:** `"exons"`
+     */
+    exons?: Field;
+
+    /**
+     * Start coordinate of the gene body.
+     *
+     * **Default:** `"start"`
+     */
+    start?: Field;
+
+    /**
+     * Field names for the flattened exons.
+     *
+     * **Default:** `["exonStart", "exonEnd"]`
+     */
+    as?: [string, string];
+}
+
+export type TransformParams =
+    | AggregateParams
+    | CollectParams
+    | CoverageParams
+    | FlattenDelimitedParams
+    | FormulaParams
+    | FilterParams
+    | FilterScoredLabelsParams
+    | FlattenParams
+    | FlattenCompressedExonsParams
+    | FlattenSequenceParams
+    | IdentifierParams
+    | LinearizeGenomicCoordinateParams
+    | MeasureTextParams
+    | MergeFacetsParams
+    | PileupParams
+    | ProjectParams
+    | RegexExtractParams
+    | RegexFoldParams
+    | SampleParams
+    | StackParams;

package/dist/src/spec/view.d.ts

@@ -0,0 +1,214 @@
+import { Data } from "./data";
+import { TransformParams } from "./transform";
+import {
+    Channel,
+    Encoding,
+    FacetFieldDef,
+    PrimaryPositionalChannel,
+} from "./channel";
+import {
+    FillAndStrokeProps,
+    MarkConfigAndType,
+    MarkType,
+    RectProps,
+} from "./mark";
+import { Title } from "./title";
+import { SampleSpec } from "./sampleView";
+
+export interface SizeDef {
+    /** Size in pixels */
+    px?: number;
+
+    /** Share of the remaining space */
+    grow?: number;
+}
+
+// TODO: Perhaps this should be in "utils"
+export type GeometricDimension = "width" | "height";
+
+export interface FacetMapping {
+    column?: FacetFieldDef;
+    row?: FacetFieldDef;
+}
+
+/**
+ * DynamicOpacity specifies a zoom-dependent behavior for view opacity.
+ * The opacity is interpolated between the specified stops.
+ */
+export interface DynamicOpacity {
+    channel?: PrimaryPositionalChannel;
+    /** Stops expressed as units (base pairs, for example) per pixel. */
+    unitsPerPixel: number[];
+    /** Opacity values that match the given stops. */
+    values: number[];
+}
+
+export type ViewOpacityDef = number | DynamicOpacity;
+
+export interface Step {
+    step: number;
+}
+
+export type Side = "top" | "right" | "bottom" | "left";
+
+export type Paddings = Partial<Record<Side, number>>;
+
+export type PaddingConfig = Paddings | number;
+
+interface CompleteViewBackground extends RectProps, FillAndStrokeProps {
+    // TODO: style?: string | string[];
+
+    // TODO: Move to FillAndStrokeProps or something
+    strokeWidth?: number;
+}
+
+export type ViewBackground = Pick<
+    CompleteViewBackground,
+    "fill" | "fillOpacity" | "stroke" | "strokeWidth" | "strokeOpacity"
+>;
+
+export interface ViewSpecBase extends ResolveSpec {
+    name?: string;
+
+    height?: SizeDef | number | Step | "container";
+    width?: SizeDef | number | Step | "container";
+
+    /**
+     * Padding in pixels.
+     *
+     * **Default:* `0`
+     */
+    padding?: PaddingConfig;
+
+    data?: Data;
+    transform?: TransformParams[];
+    encoding?: Encoding;
+    title?: string | Title;
+
+    /**
+     * A description of the view. Multiple lines can be provided as an array.
+     */
+    description?: string | string[];
+
+    baseUrl?: string;
+
+    /**
+     * Opacity of the view and all its children.
+     *
+     * **Default:* `1.0`
+     */
+    // TODO: Should be available only in Unit and Layer views.
+    opacity?: ViewOpacityDef;
+
+    /**
+     * Visibility of the view. An invisible view is removed from the layout
+     * and not rendered.
+     *
+     * **Default:** `true`
+     */
+    // TODO: Detach invisible views from the data flow.
+    visible?: boolean;
+
+    /**
+     * Is the visibility configurable interactively from the App.
+     * Configurability requires that the view has an explicitly specified name
+     * that is *unique* in within the view specification.
+     *
+     * **Default:** `false` for children of `layer`, `true` for others.
+     */
+    configurableVisibility?: boolean;
+}
+
+export interface UnitSpec extends ViewSpecBase, AggregateSamplesSpec {
+    view?: ViewBackground;
+    mark: MarkType | MarkConfigAndType;
+}
+
+export interface AggregateSamplesSpec {
+    // TODO: Introduce a type (UnitSpec | LayerSpec) that can ba used in SampleView and here
+    aggregateSamples?: (UnitSpec | LayerSpec)[];
+}
+
+export interface LayerSpec extends ViewSpecBase, AggregateSamplesSpec {
+    view?: ViewBackground;
+    layer: (LayerSpec | UnitSpec)[];
+}
+
+export interface FacetSpec extends ViewSpecBase {
+    facet: any; //FacetMapping | FacetFieldDef
+    spec: LayerSpec | UnitSpec;
+    columns?: number;
+    spacing?: number;
+}
+
+export type ResolutionTarget = "scale" | "axis";
+
+/**
+ * `"independent"` and `"shared"` behave similarly to Vega-Lite.
+ * `"excluded"` behaves like `"shared"`, but is not pulled towards the root.
+ * `"forced"` behaves like `"shared"`, but is forced towards the root even
+ * if the parent has `"independent"` behavior.
+ */
+export type ResolutionBehavior =
+    | "independent"
+    | "shared"
+    | "excluded"
+    | "forced";
+
+export interface ResolveSpec {
+    resolve?: Partial<
+        Record<
+            ResolutionTarget,
+            Partial<Record<Channel | "default", ResolutionBehavior>>
+        >
+    >;
+}
+
+export type ContainerSpec = (
+    | LayerSpec
+    //    | FacetSpec
+    | SampleSpec
+    | VConcatSpec
+    | HConcatSpec
+    | ConcatSpec
+    | UnitSpec
+) &
+    ResolveSpec;
+
+export type ViewSpec =
+    | UnitSpec
+    | LayerSpec
+    //    | FacetSpec
+    | SampleSpec
+    | VConcatSpec
+    | HConcatSpec
+    | ConcatSpec;
+
+export interface ImportConfig {
+    name?: string;
+    url?: string;
+    params?: object;
+}
+
+export interface ImportSpec {
+    import: ImportConfig;
+}
+
+export interface ConcatBase extends ViewSpecBase {
+    spacing?: number;
+}
+
+export interface VConcatSpec extends ConcatBase {
+    vconcat: (ViewSpec | ImportSpec)[];
+}
+
+export interface HConcatSpec extends ConcatBase {
+    hconcat: (ViewSpec | ImportSpec)[];
+}
+
+export interface ConcatSpec extends ConcatBase {
+    concat: (ViewSpec | ImportSpec)[];
+    columns: number;
+}
+
+export type AnyConcatSpec = VConcatSpec | HConcatSpec | ConcatSpec;

package/dist/src/styles/genome-spy.css.d.ts

@@ -0,0 +1,3 @@
+export default css;
+declare const css: ".genome-spy {\n  font-family: system-ui, \"Segoe UI\", Roboto, Helvetica, Arial, sans-serif, \"Apple Color Emoji\", \"Segoe UI Emoji\", \"Segoe UI Symbol\";\n  position: relative;\n}\n.genome-spy canvas {\n  transform: scale(1, 1);\n  opacity: 1;\n  transition: transform 0.6s, opacity 0.6s;\n}\n.genome-spy .loading-message {\n  position: absolute;\n  top: 0;\n  bottom: 0;\n  left: 0;\n  right: 0;\n  display: flex;\n  align-items: center;\n  justify-content: center;\n}\n.genome-spy .loading-message .message {\n  color: #666;\n  opacity: 0;\n  transition: opacity 0.7s;\n}\n.genome-spy.loading canvas {\n  transform: scale(0.95, 0.95);\n  opacity: 0;\n}\n.genome-spy.loading .loading-message .message {\n  opacity: 1;\n}\n.genome-spy.loading .ellipsis {\n  animation: blinker 1s linear infinite;\n}\n@keyframes blinker {\n  50% {\n    opacity: 0;\n  }\n}\n.genome-spy .tooltip {\n  position: absolute;\n  max-width: 450px;\n  overflow: hidden;\n  background: #f6f6f6;\n  padding: 10px;\n  font-size: 13px;\n  box-shadow: 0px 3px 15px 0px rgba(0, 0, 0, 0.21);\n  pointer-events: none;\n  z-index: 100;\n}\n.genome-spy .tooltip > :last-child {\n  margin-bottom: 0;\n}\n.genome-spy .tooltip > .title {\n  padding-bottom: 5px;\n  margin-bottom: 5px;\n  border-bottom: 1px dashed #b6b6b6;\n}\n.genome-spy .tooltip .summary {\n  font-size: 12px;\n}\n.genome-spy .tooltip table {\n  border-collapse: collapse;\n}\n.genome-spy .tooltip table:first-child {\n  margin-top: 0;\n}\n.genome-spy .tooltip table th,\n.genome-spy .tooltip table td {\n  padding: 2px 0.4em;\n  vertical-align: top;\n}\n.genome-spy .tooltip table th:first-child,\n.genome-spy .tooltip table td:first-child {\n  padding-left: 0;\n}\n.genome-spy .tooltip table th {\n  text-align: left;\n  font-weight: bold;\n}\n.genome-spy .tooltip .color-legend {\n  display: inline-block;\n  width: 0.8em;\n  height: 0.8em;\n  margin-left: 0.4em;\n  box-shadow: 0px 0px 3px 1px white;\n}\n.genome-spy .tooltip .attributes .hovered {\n  background-color: #e0e0e0;\n}\n.genome-spy .tooltip .na {\n  color: #aaa;\n  font-style: italic;\n  font-size: 80%;\n}\n.genome-spy .gene-track-tooltip .summary {\n  font-size: 90%;\n}\n.genome-spy .message-box {\n  display: flex;\n  align-items: center;\n  justify-content: center;\n  position: absolute;\n  top: 0;\n  height: 100%;\n  width: 100%;\n}\n.genome-spy .message-box > div {\n  border: 1px solid red;\n  padding: 10px;\n  background: #fff0f0;\n}";
+//# sourceMappingURL=genome-spy.css.d.ts.map