npm - @weng-lab/visualization - Versions diffs - 1.2.11 → 1.3.0-beta.0 - Mend

@weng-lab/visualization 1.2.11 → 1.3.0-beta.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (38) hide show

package/dist/src/components/PhyloTree/example-data/241_mammals_treedata.d.ts.map ADDED Viewed

@@ -0,0 +1 @@

+ {"version":3,"file":"241_mammals_treedata.d.ts","sourceRoot":"","sources":["../../../../../src/components/PhyloTree/example-data/241_mammals_treedata.ts"],"names":[],"mappings":"AAAA,eAAO,MAAM,IAAI;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;CAm2EhB,CAAA"}

package/dist/src/components/PhyloTree/example-data/utils.d.ts ADDED Viewed

@@ -0,0 +1,6 @@
+export declare const speciesOrderInApiData: string[];
+export declare const getLabel: (id: string) => string;
+export declare const getColor: (id: string) => string;
+export declare const getOrder: (id: string) => "PRIMATES" | "DERMOPTERA" | "CARNIVORA" | "LAGOMORPHA" | "CETARTIODACTYLA" | "RODENTIA" | "HYRACOIDEA" | "PERISSODACTYLA" | "CHIROPTERA" | "EULIPOTYPHLA" | "PHOLIDOTA" | "PILOSA" | "AFROSORICIDA" | "SIRENIA" | "TUBULIDENTATA" | "PROBOSCIDEA" | "SCANDENTIA" | "CINGULATA" | "MACROSCELIDEA" | undefined;
+export declare const sortByOrder: (speciesA: string, speciesB: string) => number;
+//# sourceMappingURL=utils.d.ts.map

package/dist/src/components/PhyloTree/example-data/utils.d.ts.map ADDED Viewed

	@@ -0,0 +1 @@
1	+ {"version":3,"file":"utils.d.ts","sourceRoot":"","sources":["../../../../../src/components/PhyloTree/example-data/utils.ts"],"names":[],"mappings":"AAwBA,eAAO,MAAM,qBAAqB,UAkPjC,CAAC;AA0CF,eAAO,MAAM,QAAQ,GAAI,IAAI,MAAM,WAIlC,CAAC;AAEF,eAAO,MAAM,QAAQ,GAAI,IAAI,MAAM,WAKlC,CAAC;AAEF,eAAO,MAAM,QAAQ,GAAI,IAAI,MAAM,iTAIlC,CAAC;AAEF,eAAO,MAAM,WAAW,GAAI,UAAU,MAAM,EAAE,UAAU,MAAM,WAM7D,CAAA"}

package/dist/src/components/PhyloTree/index.d.ts ADDED Viewed

@@ -0,0 +1,4 @@
+import { default as PhyloTree } from './PhyloTree';
+export { PhyloTree };
+export type { TreeItem, PhyloTreeProps } from './types';
+//# sourceMappingURL=index.d.ts.map

package/dist/src/components/PhyloTree/index.d.ts.map ADDED Viewed

	@@ -0,0 +1 @@
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package/dist/src/components/PhyloTree/types.d.ts ADDED Viewed

@@ -0,0 +1,106 @@
+import { TransformMatrix } from '@visx/zoom/lib/types';
+import { HierarchyPointNode } from 'd3-hierarchy';
+import { ReactNode } from 'react';
+export type ZoomState = {
+    initialTransformMatrix: TransformMatrix;
+    transformMatrix: TransformMatrix;
+    isDragging: boolean;
+};
+export type TreeItem = {
+    id: string;
+    branch_length: number | null;
+    children?: TreeItem[];
+};
+/**
+ * Internal only, used for layout precalculation
+ */
+export interface TreeNode extends HierarchyPointNode<TreeItem> {
+    cumulativeBranchLength?: number;
+    baseNodeX?: number;
+    baseNodeY?: number;
+    scaledNodeX?: number;
+    scaledNodeY?: number;
+    branchLengthScaledRadius?: number;
+    baseLinkPath?: string;
+    scaledLinkPath?: string;
+    linkStrokeWidth?: number;
+    labelStrokeWidth?: number;
+    baseLeafLinkExtension?: {
+        x1: number;
+        x2: number;
+        y1: number;
+        y2: number;
+    };
+    scaledLeafLinkExtension?: {
+        x1: number;
+        x2: number;
+        y1: number;
+        y2: number;
+    };
+    label?: string;
+    color?: string;
+    lightenedLinkExtColor?: string;
+    ancestorIds?: Set<string>;
+    descendantIds?: Set<string>;
+}
+export type TreeLink = {
+    source: TreeNode;
+    target: TreeNode;
+};
+export type PhyloTreeProps = {
+    width: number;
+    height: number;
+    data: TreeItem;
+    /**
+     * `id` of TreeItem(s) to be highlighted
+     */
+    highlighted?: string[];
+    /**
+     * Used to sync plot state with hover on SequenceAlignmentPlot. Tree treats these as if they are internally hovered
+     */
+    hovered?: string[];
+    /**
+     * @default 135
+     */
+    labelPadding?: number;
+    /**
+     * @default
+     * (id: string) => id
+     */
+    getLabel?: (id: string) => string;
+    /**
+     * @default
+     * (id: string) => 'black'
+     */
+    getColor?: (id: string) => string;
+    /**
+     * Optionally define tooltip for hover over leaf nodes
+     */
+    tooltipContents?: (id: string) => ReactNode;
+    /**
+     * fired when individual leaf node clicked
+     */
+    onLeafClick?: (id: string) => void;
+    /**
+     * Fired when hover state changes, single item if leaf hovered, multiple if branch hovered, empty on mouse leave
+     */
+    onLeafHoverChange?: (hovered: string[]) => void;
+    /**
+     * Whether or not to use branch length on initial load
+     * @default "scaled"
+     */
+    defaultScaling?: "unscaled" | "scaled";
+    /**
+     * @default 8
+     */
+    leafFontSize?: number;
+    /**
+     * @default 'Arial'
+     */
+    leafFontFamily?: string;
+    /**
+     * @default 1
+     */
+    linkStrokeWidth?: number;
+};
+//# sourceMappingURL=types.d.ts.map

package/dist/src/components/PhyloTree/types.d.ts.map ADDED Viewed

@@ -0,0 +1 @@

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package/dist/src/components/ScatterPlot/scatterplot.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"scatterplot.d.ts","sourceRoot":"","sources":["../../../../src/components/ScatterPlot/scatterplot.tsx"],"names":[],"mappings":"AAIA,OAAO,EAAE,UAAU,EAAgC,MAAM,SAAS,CAAC;AA8BnE,QAAA,MAAM,WAAW,GAAI,CAAC,SAAS,MAAM,EAAE,CAAC,SAAS,OAAO,GAAG,SAAS,GAAG,SAAS,EAAE,CAAC,SAAS,OAAO,GAAG,SAAS,GAAG,SAAS,EACvH,OAAO,UAAU,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,CAAC,4CAwsB7B,CAAA;AAED,eAAe,WAAW,CAAC"}

package/dist/src/components/ScatterPlot/types.d.ts CHANGED Viewed

@@ -1,7 +1,7 @@
 import { ScaleLinear } from '@visx/vendor/d3-scale';
 import { ProvidedZoom } from '@visx/zoom/lib/types';
 import { ReactElement } from 'react';
-import { DownloadPlotHandle, AnimationType } from '../../utility';
+import { DownloadPlotHandle } from '../../utility';
 type Download = "none" | "inline" | "topRight" | "topLeft" | "bottomRight" | "bottomLeft";
 /**
     All information given to a point on the plot, including its coordinates(x and y), its radius, color, and opacity, and its metadata information
@@ -208,9 +208,6 @@ export type ChartProps<T, S extends boolean | undefined, Z extends boolean | und
      * Default none
      */
     downloadButton?: Download;
-    animation?: AnimationType;
-    animationBuffer?: number;
-    animationGroupSize?: number;
 };
 export type Line = {
     x: number;

package/dist/src/components/ScatterPlot/types.d.ts.map CHANGED Viewed

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package/dist/src/components/SequenceAlignmentPlot/SequenceAlignmentPlot.d.ts ADDED Viewed

@@ -0,0 +1,47 @@
+import { default as React, ReactNode } from 'react';
+export type Nucleotide = "A" | "C" | "G" | "T" | "-";
+export interface SequenceAlignmentPlotProps {
+    data: {
+        [id: string]: Nucleotide[];
+    };
+    getLabel: (id: string) => string;
+    getOrderColor: (id: string) => string;
+    /**
+     * the evolutionary order, not sort order. Sort in plot by sorting input data
+     */
+    getOrder: (id: string) => string;
+    width: number;
+    height: number;
+    /**
+     * Used to sync plot state with hover on PhyloTree. Plot treats these as if they are internally hovered
+     */
+    hovered?: string[];
+    /**
+     * Fired when internal hover state changes
+     */
+    onHoverChange?: (hovered: string | null) => void;
+    /**
+     * Places indicator next to species
+     */
+    highlighted?: string[];
+    /**
+     * Optionally define tooltip for hover over leaf nodes
+     */
+    tooltipContents?: (tooltipData: TooltipData) => ReactNode;
+}
+export type SpeciesInfo = {
+    id: string;
+    label: string;
+    order: string;
+    color: string;
+};
+export type TooltipData = SpeciesInfo & {
+    basePair?: Nucleotide;
+    position?: number;
+};
+/**
+ * @todo This component could use some cleanup and maybe manual memoization to handle hover changes to highlight more efficiently
+ * Maybe try debouncing the hover changes using requestAnimationFrame like PhyloTree
+ */
+export declare const SequenceAlignmentPlot: React.FC<SequenceAlignmentPlotProps>;
+//# sourceMappingURL=SequenceAlignmentPlot.d.ts.map

package/dist/src/components/SequenceAlignmentPlot/SequenceAlignmentPlot.d.ts.map ADDED Viewed

@@ -0,0 +1 @@

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package/dist/src/components/SequenceAlignmentPlot/example-data/mockData.d.ts ADDED Viewed

@@ -0,0 +1,25 @@
+export declare const EH38E3465364: {
+    data: {
+        ccreSequenceAlignmentQuery: {
+            sequence_alignment: number[][];
+            accession: string;
+        }[];
+    };
+};
+export declare const EH38E4276533: {
+    data: {
+        ccreSequenceAlignmentQuery: {
+            sequence_alignment: number[][];
+            accession: string;
+        }[];
+    };
+};
+export declare const EH38E4276534: {
+    data: {
+        ccreSequenceAlignmentQuery: {
+            sequence_alignment: number[][];
+            accession: string;
+        }[];
+    };
+};
+//# sourceMappingURL=mockData.d.ts.map

package/dist/src/components/SequenceAlignmentPlot/example-data/mockData.d.ts.map ADDED Viewed

	@@ -0,0 +1 @@
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package/dist/src/components/SequenceAlignmentPlot/index.d.ts ADDED Viewed

	@@ -0,0 +1,2 @@
1	+ export * from './SequenceAlignmentPlot';
2	+ //# sourceMappingURL=index.d.ts.map

package/dist/src/components/SequenceAlignmentPlot/index.d.ts.map ADDED Viewed

	@@ -0,0 +1 @@
1	+ {"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../../src/components/SequenceAlignmentPlot/index.ts"],"names":[],"mappings":"AAAA,cAAc,yBAAyB,CAAA"}

package/dist/src/index.d.ts CHANGED Viewed

@@ -11,4 +11,6 @@ export type { TreemapNode, TreemapProps } from './components/TreeMap';
 export type { DownloadPlotHandle } from './utility';
 export { ProportionsBar, getProportionsFromArray } from './components/ProportionsBar';
 export type { ProportionsBarProps } from './components/ProportionsBar';
+export * from './components/PhyloTree';
+export * from './components/SequenceAlignmentPlot';
 //# sourceMappingURL=index.d.ts.map

package/dist/src/index.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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