hyphy-scope
Version:
Reusable Svelte components for HyPhy analysis visualization
75 lines (74 loc) • 2.35 kB
TypeScript
export interface MemeResults {
MLE: {
content: Record<string, number[][]>;
headers: [string, string][];
LRT?: Record<string, number[][]>;
};
"data partitions": Record<string, {
coverage: [number[]];
}>;
input: {
"number of sequences": number;
"number of sites": number;
"partition count": number;
};
analysis: {
citation: string;
version?: string;
};
tested?: any[];
substitutions?: any;
"branch attributes"?: any;
}
export interface MemeAttributes {
testedBranchCount: number;
hasResamples: number;
hasSubstitutions: boolean;
hasSiteLRT: boolean;
hasBackground: boolean;
siteIndexPartitionCodon: [number, number][];
numberOfSequences: number;
numberOfSites: number;
numberOfPartitions: number;
partitionSizes: number[];
}
export interface MemeSiteData {
Partition: number;
Codon: number;
alpha: number;
"beta-": number;
"p-": number;
"beta+": number;
"p+": number;
"p-value": number;
"Branches": number;
class: "Diversifying" | "Neutral" | "Invariable";
[key: string]: any;
}
export interface TileSpec {
number: number | string;
description: string;
icon: string;
color: string;
}
export declare const MEME_COLORS: {
Diversifying: string;
Neutral: string;
Invariable: string;
};
export declare function getMemeAttributes(resultsJson: MemeResults): MemeAttributes;
export declare function getMemeCountSitesByPvalue(resultsJson: MemeResults, pvalueThreshold: number): number;
export declare function getMemeSelectedBranchesPerSelectedSite(resultsJson: MemeResults, pvalueThreshold: number): string | number;
export declare function getMemeTileSpecs(resultsJson: MemeResults, pvalueThreshold: number): TileSpec[];
export declare function getMemeSiteTableData(resultsJson: MemeResults, pvalueThreshold: number): [MemeSiteData[], any[], any];
export declare function getMemeOmegaPlot(record: number[]): Array<{
value: number;
weight: number;
}>;
export declare function getMemePosteriorsPerBranchSite(resultsJson: MemeResults, rateClass?: number): Array<{
Branch: string;
Codon: number;
Posterior: number;
ER: number;
}>;
export declare function getMemeComputeER(prior: number, posterior: number): number;