@weng-lab/visualization 1.2.12 → 1.3.0-beta.1

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

@@ -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

@@ -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

@@ -0,0 +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

@@ -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

@@ -0,0 +1 @@
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../../src/components/PhyloTree/index.ts"],"names":[],"mappings":"AAAA,OAAO,SAAS,MAAM,aAAa,CAAA;AACnC,OAAO,EAAE,SAAS,EAAE,CAAC;AACrB,YAAY,EAAE,QAAQ,EAAE,cAAc,EAAE,MAAM,SAAS,CAAC"}

package/dist/src/components/PhyloTree/types.d.ts

@@ -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

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

@@ -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

@@ -0,0 +1 @@
+{"version":3,"file":"SequenceAlignmentPlot.d.ts","sourceRoot":"","sources":["../../../../src/components/SequenceAlignmentPlot/SequenceAlignmentPlot.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAqD,SAAS,EAAE,MAAM,OAAO,CAAC;AAO5F,MAAM,MAAM,UAAU,GAAG,GAAG,GAAG,GAAG,GAAG,GAAG,GAAG,GAAG,GAAG,GAAG,CAAC;AAUrD,MAAM,WAAW,0BAA0B;IACzC,IAAI,EAAE;QAAE,CAAC,EAAE,EAAE,MAAM,GAAG,UAAU,EAAE,CAAA;KAAE,CAAC;IACrC,QAAQ,EAAE,CAAC,EAAE,EAAE,MAAM,KAAK,MAAM,CAAC;IACjC,aAAa,EAAE,CAAC,EAAE,EAAE,MAAM,KAAK,MAAM,CAAC;IACtC;;OAEG;IACH,QAAQ,EAAE,CAAC,EAAE,EAAE,MAAM,KAAK,MAAM,CAAC;IACjC,KAAK,EAAE,MAAM,CAAC;IACd,MAAM,EAAE,MAAM,CAAC;IACf;;OAEG;IACH,OAAO,CAAC,EAAE,MAAM,EAAE,CAAC;IACnB;;OAEG;IACH,aAAa,CAAC,EAAE,CAAC,OAAO,EAAE,MAAM,GAAG,IAAI,KAAK,IAAI,CAAC;IACjD;;OAEG;IACH,WAAW,CAAC,EAAE,MAAM,EAAE,CAAC;IACvB;;OAEG;IACH,eAAe,CAAC,EAAE,CAAC,WAAW,EAAE,WAAW,KAAK,SAAS,CAAC;CAC3D;AAYD,MAAM,MAAM,WAAW,GAAG;IAAE,EAAE,EAAE,MAAM,CAAC;IAAC,KAAK,EAAE,MAAM,CAAC;IAAC,KAAK,EAAE,MAAM,CAAC;IAAC,KAAK,EAAE,MAAM,CAAA;CAAE,CAAC;AAEtF,MAAM,MAAM,WAAW,GAAG,WAAW,GAAG;IACtC,QAAQ,CAAC,EAAE,UAAU,CAAC;IACtB,QAAQ,CAAC,EAAE,MAAM,CAAC;CACnB,CAAC;AAcF;;;GAGG;AACH,eAAO,MAAM,qBAAqB,EAAE,KAAK,CAAC,EAAE,CAAC,0BAA0B,CA6VtE,CAAC"}

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

@@ -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

@@ -0,0 +1 @@
+{"version":3,"file":"mockData.d.ts","sourceRoot":"","sources":["../../../../../src/components/SequenceAlignmentPlot/example-data/mockData.ts"],"names":[],"mappings":"AAAA,eAAO,MAAM,YAAY;;;;;;;CAs1FxB,CAAC;AAEF,eAAO,MAAM,YAAY;;;;;;;CAs1FxB,CAAC;AAEF,eAAO,MAAM,YAAY;;;;;;;CAs1FxB,CAAC"}

package/dist/src/components/SequenceAlignmentPlot/index.d.ts

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

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

@@ -0,0 +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

@@ -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

@@ -1 +1 @@
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+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,WAAW,EAAE,MAAM,0BAA0B,CAAC;AACvD,YAAY,EAAE,YAAY,EAAE,UAAU,EAAE,KAAK,EAAE,MAAM,0BAA0B,CAAC;AAEhF,OAAO,EAAE,KAAK,EAAE,MAAM,oBAAoB,CAAC;AAC3C,YAAY,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAC;AAErD,OAAO,EAAE,UAAU,EAAE,MAAM,yBAAyB,CAAC;AACrD,YAAY,EAAE,YAAY,EAAE,eAAe,EAAE,WAAW,EAAE,MAAM,yBAAyB,CAAC;AAE1F,OAAO,EAAE,OAAO,EAAE,MAAM,sBAAsB,CAAC;AAC/C,YAAY,EAAE,YAAY,EAAE,OAAO,EAAE,MAAM,sBAAsB,CAAC;AAElE,OAAO,EAAE,OAAO,EAAE,MAAM,sBAAsB,CAAA;AAC9C,YAAY,EAAE,WAAW,EAAE,YAAY,EAAE,MAAM,sBAAsB,CAAA;AAErE,YAAY,EAAE,kBAAkB,EAAE,MAAM,WAAW,CAAA;AAEnD,OAAO,EAAE,cAAc,EAAE,uBAAuB,EAAE,MAAM,6BAA6B,CAAC;AACtF,YAAY,EAAC,mBAAmB,EAAC,MAAM,6BAA6B,CAAA;AAEpE,cAAc,wBAAwB,CAAA;AAEtC,cAAc,oCAAoC,CAAA"}