hyphy-scope/dist/utils/absrel-utils.d.ts

Reusable Svelte components for HyPhy analysis visualization

/**
 * ABSREL (Adaptive Branch-Site Random Effects Likelihood) utility functions
 *
 * ABSREL tests whether a gene has experienced positive selection,
 * without requiring a priori specification of lineages.
 */
export interface AbsrelSiteData {
    site: number;
    partition: number;
    [branchName: string]: number;
}
export interface AbsrelBranchData {
    name: string;
    'Rate classes': number;
    'Uncorrected P-value': number;
    'Corrected P-value': number;
    'Bayes Factor': number;
    'ω distribution': Array<{
        'rate class': number;
        omega: number;
        weight: number;
    }>;
}
export interface AbsrelResults {
    sequences: number;
    sites: number;
    'branches tested': number;
    'branches with selection': number;
    'p-value threshold': number;
    'test results': {
        [branchName: string]: {
            'Rate classes': number;
            'Uncorrected P-value': number;
            'Corrected P-value': number;
            'Bayes Factor': number;
        };
    };
    'Site Log Likelihood': {
        tested: {
            [branchName: string]: number[][];
        };
    };
    'branch attributes': {
        [branchName: string]: {
            [attribute: string]: any;
        };
    };
    fits: {
        'Baseline model': {
            'log-likelihood': number;
            AIC: number;
            parameters: number;
        };
        'Full adaptive model': {
            'log-likelihood': number;
            AIC: number;
            parameters: number;
        };
    };
    'Synonymous site-posteriors'?: {
        [branchName: string]: number[][];
    };
}
/**
 * Extract summary statistics from ABSREL results
 */
export declare function getAbsrelSummary(data: AbsrelResults | any): {
    sequences: any;
    sites: any;
    branchesTested: any;
    branchesWithSelection: any;
    pValueThreshold: any;
    baselineLogLikelihood: any;
    fullModelLogLikelihood: any;
    lrt: number;
    baselineAIC: any;
    fullModelAIC: any;
};
/**
 * Get tested branches with their selection results
 */
export declare function getTestedBranches(data: AbsrelResults | any): AbsrelBranchData[];
/**
 * Get site-level log likelihood data for visualization
 */
export declare function getAbsrelSiteData(data: AbsrelResults | any): AbsrelSiteData[];
/**
 * Filter branches by significance
 */
export declare function getSignificantBranches(branches: AbsrelBranchData[], pValueThreshold?: number): AbsrelBranchData[];
/**
 * Get table headers for ABSREL results
 */
export declare function getAbsrelTableHeaders(): Array<{
    key: string;
    label: string;
    sortable: boolean;
}>;
/**
 * Format numeric values for display
 */
export declare function formatAbsrelValue(value: any, key: string): string;
/**
 * Get color for p-value significance
 */
export declare function getPValueColor(pValue: number, threshold?: number): string;
/**
 * Extract synonymous site posteriors if available
 */
export declare function getSynonymousSitePosteriors(data: AbsrelResults): {
    [branchName: string]: number[][];
};
/**
 * Calculate evidence ratio for branches
 */
export declare function calculateEvidenceRatio(bayesFactor: number): number;
/**
 * Extract comprehensive attributes from aBSREL results for visualization
 */
export interface AbsrelAttributes {
    positiveResults: number;
    pvalueThreshold: number;
    profilableBranches: Set<string>;
    testedBranchCount: number;
    srvRateClasses: number;
    srvDistribution: Array<{
        value: number;
        weight: number;
    }> | null;
    omegaRateClasses: number[];
    mhRates: {
        DH: number;
        TH: number;
    };
    profileBranchSites: AbsrelProfileSite[];
    numberOfSequences: number;
    numberOfSites: number;
    numberOfPartitions: number;
    partitionSizes: number[];
}
export interface AbsrelProfileSite {
    Key: string;
    branch: string;
    site: number;
    ER: number;
    subs: number;
    from: string;
    to: string;
    syn_subs: number;
    nonsyn_subs: number;
}
export interface AbsrelBranchSiteData {
    Key: string;
    Posterior: number;
    ER: number;
    subs: number;
    from: string;
    to: string;
    syn_subs: number;
    nonsyn_subs: number;
}
export interface AbsrelDistributionTableRow {
    branch: string;
    tested: string;
    'p-value': number | null;
    sites: number | null;
    rates: number;
    dist: [string, Array<{
        value: number;
        weight: number;
    }>, string];
    plot: [string, Array<{
        value: number;
        weight: number;
    }>];
}
/**
 * Extract comprehensive attributes from ABSREL results
 */
export declare function getAbsrelAttributes(resultsJson: any): AbsrelAttributes;
/**
 * Profile branch sites by calculating metrics based on log likelihoods
 */
export declare function getAbsrelProfileBranchSites(resultsJson: any): AbsrelProfileSite[];
/**
 * Create table specs for tile display
 */
export declare function getAbsrelTileSpecs(resultsJson: any, evThreshold: number, distributionTable: AbsrelDistributionTableRow[]): any[];
/**
 * Get rate distribution for a branch
 */
export declare function getAbsrelTestOmega(resultsJson: any, branch: string): Array<{
    value: number;
    weight: number;
}>;
/**
 * Get site index to partition and codon mapping
 */
export declare function getAbsrelSiteIndexPartitionCodon(resultsJson: any): Array<[number, number]>;
/**
 * Get branch color options for tree visualization
 */
export declare function getAbsrelTreeColorOptions(resultsJson: any, evThreshold: number): string[];
/**
 * Tree configuration options for ABSREL visualization
 */
export interface AbsrelTreeOptions {
    branchLabels?: boolean;
    neighbors?: boolean;
    height?: number;
    width?: number;
    alignTips?: boolean;
    showScale?: boolean;
    isRadial?: boolean;
    showInternal?: boolean;
    colorBranches?: string;
    branchLength?: string;
    evThreshold?: number;
}
/**
 * Create tree configuration for ABSREL visualization
 */
export declare function createAbsrelTreeConfig(resultsJson: any, partitionIndex?: number, options?: AbsrelTreeOptions): any;
/**
 * Get distribution table for branches
 */
export declare function getAbsrelDistributionTable(resultsJson: any, evThreshold: number): AbsrelDistributionTableRow[];
/**
 * Generate site table data for detailed analysis
 */
export declare function getAbsrelSiteTableData(resultsJson: any, evThreshold: number, profileBranchSites?: AbsrelProfileSite[]): [any[], {
    [key: string]: any;
}];