npm - agentic-flow - Versions diffs - 1.9.0 → 1.9.1 - Mend

agentic-flow 1.9.0 → 1.9.1

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package/agentic-flow/examples/crispr-cas13-pipeline/docs/algorithms/reporting-module.md DELETED Viewed

@@ -1,1135 +0,0 @@
-# Reporting Engine - Detailed Pseudocode
-## Overview
-The Reporting Engine aggregates results from all pipeline modules and generates comprehensive visualizations, interactive reports, and data exports in standard bioinformatics formats.
----
-## Algorithm 1: Report Data Aggregation
-**Purpose**: Collect and structure data from all pipeline components.
-```
-ALGORITHM: AggregateReportData
-INPUT: alignmentResults, offTargetResults, expressionResults, config
-OUTPUT: aggregatedData (ReportData object)
-BEGIN
-    reportData ← {
-        metadata: {},
-        alignment: {},
-        offTarget: {},
-        expression: {},
-        qualityMetrics: {},
-        timestamp: GetCurrentTime()
-    }
-    // Step 1: Extract metadata
-    reportData.metadata ← {
-        projectName: config.projectName,
-        analysisDate: FormatDate(GetCurrentTime()),
-        pipelineVersion: config.version,
-        referenceGenome: config.referenceGenome,
-        organism: config.organism,
-        experimentType: config.experimentType
-    }
-    // Step 2: Aggregate alignment statistics
-    reportData.alignment ← {
-        totalReads: alignmentResults.statistics.totalReads,
-        alignedReads: alignmentResults.statistics.alignedReads,
-        alignmentRate: alignmentResults.statistics.alignmentRate × 100,
-        unmappedReads: alignmentResults.statistics.unmappedReads,
-        multiMappedReads: alignmentResults.statistics.multiMappedReads,
-        averageAlignmentScore: CalculateAverageAlignmentScore(alignmentResults),
-        averageMAPQ: CalculateAverageMAPQ(alignmentResults),
-        coverageStatistics: CalculateCoverageStatistics(alignmentResults)
-    }
-    // Step 3: Aggregate off-target predictions
-    IF offTargetResults != null THEN
-        reportData.offTarget ← {
-            totalGRNAs: length(offTargetResults.gRNAs),
-            totalCandidateSites: SUM(length(g.candidates) for g in offTargetResults.gRNAs),
-            totalPredictedOffTargets: SUM(length(g.predicted) for g in offTargetResults.gRNAs),
-            highConfidenceOffTargets: COUNT_HIGH_CONFIDENCE(offTargetResults),
-            topOffTargetGenes: ExtractTopOffTargetGenes(offTargetResults, topN = 20),
-            averageOffTargetScore: CalculateAverageOffTargetScore(offTargetResults)
-        }
-    END IF
-    // Step 4: Aggregate expression analysis
-    IF expressionResults != null THEN
-        reportData.expression ← {
-            totalGenesTested: expressionResults.statistics.totalGenesTested,
-            significantDEGs: expressionResults.statistics.significantGenes,
-            upregulatedGenes: expressionResults.statistics.upregulatedGenes,
-            downregulatedGenes: expressionResults.statistics.downregulatedGenes,
-            topDEGs: ExtractTopDEGs(expressionResults, topN = 50),
-            enrichedPathways: expressionResults.enrichment.pathways,
-            immuneScore: expressionResults.enrichment.immuneScore,
-            pathwayCategories: GroupPathwaysByCategory(expressionResults.enrichment)
-        }
-    END IF
-    // Step 5: Calculate quality metrics
-    reportData.qualityMetrics ← {
-        dataQuality: AssessDataQuality(alignmentResults, expressionResults),
-        sampleCorrelations: CalculateSampleCorrelations(expressionResults),
-        replicateConsistency: CalculateReplicateConsistency(expressionResults),
-        batchEffects: DetectBatchEffects(expressionResults)
-    }
-    // Step 6: Add processing statistics
-    reportData.processingStats ← {
-        alignmentTime: alignmentResults.statistics.processingTime,
-        offTargetTime: offTargetResults.statistics.processingTime,
-        expressionTime: expressionResults.statistics.processingTime,
-        totalTime: alignmentResults.statistics.processingTime +
-                   offTargetResults.statistics.processingTime +
-                   expressionResults.statistics.processingTime,
-        memoryPeak: GetPeakMemoryUsage()
-    }
-    LogInfo("Report data aggregation complete")
-    RETURN reportData
-END
-SUBROUTINE: CalculateCoverageStatistics
-INPUT: alignmentResults
-OUTPUT: coverageStats (object)
-BEGIN
-    // Calculate genome-wide coverage statistics
-    coverages ← ExtractPerBaseCoverage(alignmentResults.bamFile)
-    coverageStats ← {
-        meanCoverage: MEAN(coverages),
-        medianCoverage: MEDIAN(coverages),
-        coverage10x: PERCENTAGE(coverages >= 10),
-        coverage30x: PERCENTAGE(coverages >= 30),
-        coverage100x: PERCENTAGE(coverages >= 100),
-        stdDev: STDEV(coverages),
-        uniformity: CalculateUniformity(coverages)
-    }
-    RETURN coverageStats
-END
-SUBROUTINE: ExtractTopDEGs
-INPUT: expressionResults, topN
-OUTPUT: topGenes (array)
-BEGIN
-    // Extract top genes by statistical significance and effect size
-    allGenes ← expressionResults.deResults
-    // Filter to significant genes
-    sigGenes ← [gene for gene in allGenes WHERE gene.padj < 0.05]
-    // Sort by combined score (|log2FC| × -log10(padj))
-    FOR EACH gene IN sigGenes DO
-        gene.combinedScore ← ABS(gene.log2FoldChange) × (-LOG10(gene.padj))
-    END FOR
-    sortedGenes ← Sort(sigGenes, by = combinedScore, descending = true)
-    topGenes ← sortedGenes[0 : MIN(topN, length(sortedGenes))]
-    RETURN topGenes
-END
-```
-**Complexity Analysis**:
-- **Time**: O(G + S) where G = genes, S = samples
-- **Space**: O(G + S) for statistics storage
-- **Typical Performance**: 1-5 seconds
----
-## Algorithm 2: Visualization Generation
-**Purpose**: Create publication-quality plots and charts.
-```
-ALGORITHM: GenerateVisualizations
-INPUT: reportData (ReportData object), config (VisualizationConfig)
-OUTPUT: visualizations (array of Plot objects)
-BEGIN
-    visualizations ← []
-    // === Alignment Visualizations ===
-    // 1. Alignment rate pie chart
-    alignmentPieChart ← CreatePieChart(
-        data = [
-            {label: "Aligned", value: reportData.alignment.alignedReads},
-            {label: "Unmapped", value: reportData.alignment.unmappedReads}
-        ],
-        title = "Read Alignment Distribution",
-        colors = ["#4CAF50", "#F44336"]
-    )
-    visualizations.append(alignmentPieChart)
-    // 2. Coverage histogram
-    coverageHistogram ← CreateHistogram(
-        data = reportData.alignment.coverageStatistics.distribution,
-        title = "Genome Coverage Distribution",
-        xLabel = "Coverage Depth",
-        yLabel = "Frequency",
-        bins = 50
-    )
-    visualizations.append(coverageHistogram)
-    // === Off-Target Visualizations ===
-    IF reportData.offTarget != null THEN
-        // 3. Off-target score distribution
-        offTargetScoreDist ← CreateViolin Plot(
-            data = ExtractOffTargetScores(reportData.offTarget),
-            title = "Off-Target Score Distribution by gRNA",
-            yLabel = "Off-Target Score"
-        )
-        visualizations.append(offTargetScoreDist)
-        // 4. Top off-target genes bar chart
-        topOffTargetsBar ← CreateBarChart(
-            data = reportData.offTarget.topOffTargetGenes,
-            xLabel = "Gene Symbol",
-            yLabel = "Off-Target Score",
-            title = "Top 20 Off-Target Genes",
-            orientation = "horizontal",
-            colorScale = "YlOrRd"
-        )
-        visualizations.append(topOffTargetsBar)
-    END IF
-    // === Expression Visualizations ===
-    IF reportData.expression != null THEN
-        // 5. Volcano plot
-        volcanoPlot ← GenerateVolcanoPlot(
-            expressionData = reportData.expression.topDEGs,
-            log2FCThreshold = 1.0,
-            padjThreshold = 0.05,
-            title = "Differential Gene Expression"
-        )
-        visualizations.append(volcanoPlot)
-        // 6. MA plot
-        maPlot ← GenerateMAPlot(
-            expressionData = reportData.expression.allGenes,
-            title = "MA Plot (Expression vs Fold Change)"
-        )
-        visualizations.append(maPlot)
-        // 7. Heatmap of top DEGs
-        degHeatmap ← GenerateHeatmap(
-            genes = reportData.expression.topDEGs,
-            samples = reportData.expression.samples,
-            title = "Top 50 Differentially Expressed Genes",
-            clustering = "hierarchical",
-            colorScheme = "RdBu_r"
-        )
-        visualizations.append(degHeatmap)
-        // 8. Pathway enrichment dot plot
-        pathwayDotPlot ← GeneratePathwayDotPlot(
-            pathways = reportData.expression.enrichedPathways,
-            topN = 20,
-            title = "Immune Pathway Enrichment"
-        )
-        visualizations.append(pathwayDotPlot)
-        // 9. PCA plot
-        pcaPlot ← GeneratePCAPlot(
-            expressionData = reportData.expression.normalizedCounts,
-            metadata = reportData.expression.sampleMetadata,
-            title = "Principal Component Analysis"
-        )
-        visualizations.append(pcaPlot)
-    END IF
-    // === Genome Browser Tracks ===
-    // 10. Generate IGV-compatible tracks
-    genomeBrowserTracks ← GenerateGenomeBrowserTracks(
-        alignmentData = reportData.alignment,
-        offTargetData = reportData.offTarget,
-        config = config
-    )
-    visualizations.append(genomeBrowserTracks)
-    LogInfo("Generated {length(visualizations)} visualizations")
-    RETURN visualizations
-END
-SUBROUTINE: GenerateVolcanoPlot
-INPUT: expressionData, log2FCThreshold, padjThreshold, title
-OUTPUT: plot (Plot object)
-BEGIN
-    plot ← {
-        type: "scatter",
-        title: title,
-        xLabel: "log2 Fold Change",
-        yLabel: "-log10(adjusted p-value)",
-        points: [],
-        annotations: []
-    }
-    // Process each gene
-    FOR EACH gene IN expressionData DO
-        x ← gene.log2FoldChange
-        y ← -LOG10(gene.padj)
-        // Determine point color and size based on significance
-        IF ABS(x) >= log2FCThreshold AND gene.padj < padjThreshold THEN
-            IF x > 0 THEN
-                color ← "red"
-                label ← "Upregulated"
-            ELSE
-                color ← "blue"
-                label ← "Downregulated"
-            END IF
-            size ← 8
-        ELSE
-            color ← "gray"
-            label ← "Not significant"
-            size ← 4
-        END IF
-        plot.points.append({
-            x: x,
-            y: y,
-            color: color,
-            size: size,
-            label: label,
-            geneSymbol: gene.geneSymbol,
-            tooltip: FormatGeneTooltip(gene)
-        })
-        // Annotate top genes
-        IF gene.rank <= 10 THEN
-            plot.annotations.append({
-                x: x,
-                y: y,
-                text: gene.geneSymbol,
-                fontSize: 10
-            })
-        END IF
-    END FOR
-    // Add threshold lines
-    plot.vlines ← [
-        {x: -log2FCThreshold, style: "dashed", color: "black"},
-        {x: log2FCThreshold, style: "dashed", color: "black"}
-    ]
-    plot.hlines ← [
-        {y: -LOG10(padjThreshold), style: "dashed", color: "black"}
-    ]
-    RETURN plot
-END
-SUBROUTINE: GenerateHeatmap
-INPUT: genes, samples, title, clustering, colorScheme
-OUTPUT: heatmap (Plot object)
-BEGIN
-    // Extract expression matrix
-    expressionMatrix ← []
-    geneLabels ← []
-    FOR EACH gene IN genes DO
-        row ← [gene.normalizedCounts[sample] for sample in samples]
-        expressionMatrix.append(row)
-        geneLabels.append(gene.geneSymbol)
-    END FOR
-    // Z-score normalization for better visualization
-    normalizedMatrix ← []
-    FOR EACH row IN expressionMatrix DO
-        mean ← MEAN(row)
-        std ← STDEV(row)
-        normalizedRow ← [(value - mean) / std for value in row]
-        normalizedMatrix.append(normalizedRow)
-    END FOR
-    // Perform hierarchical clustering
-    IF clustering == "hierarchical" THEN
-        geneTree ← HierarchicalClustering(normalizedMatrix, metric = "euclidean")
-        sampleTree ← HierarchicalClustering(TRANSPOSE(normalizedMatrix), metric = "correlation")
-        // Reorder based on clustering
-        geneOrder ← GetDendrogram Order(geneTree)
-        sampleOrder ← GetDendrogramOrder(sampleTree)
-        normalizedMatrix ← ReorderMatrix(normalizedMatrix, geneOrder, sampleOrder)
-        geneLabels ← [geneLabels[i] for i in geneOrder]
-        samples ← [samples[i] for i in sampleOrder]
-    END IF
-    heatmap ← {
-        type: "heatmap",
-        title: title,
-        data: normalizedMatrix,
-        rowLabels: geneLabels,
-        colLabels: samples,
-        colorScheme: colorScheme,
-        colorBarLabel: "Z-score",
-        dendrograms: {
-            row: geneTree IF clustering != null,
-            col: sampleTree IF clustering != null
-        }
-    }
-    RETURN heatmap
-END
-SUBROUTINE: GeneratePathwayDotPlot
-INPUT: pathways, topN, title
-OUTPUT: plot (Plot object)
-BEGIN
-    // Sort pathways by adjusted p-value
-    sortedPathways ← Sort(pathways, by = padjusted, ascending = true)
-    topPathways ← sortedPathways[0 : MIN(topN, length(sortedPathways))]
-    plot ← {
-        type: "dotplot",
-        title: title,
-        xLabel: "Gene Ratio",
-        yLabel: "Pathway",
-        points: []
-    }
-    FOR EACH pathway IN topPathways DO
-        geneRatio ← pathway.overlapSize / pathway.pathwaySize
-        plot.points.append({
-            y: pathway.name,
-            x: geneRatio,
-            size: pathway.overlapSize × 2,  // Scale dot size by overlap
-            color: -LOG10(pathway.padjusted),  // Color by significance
-            tooltip: FormatPathwayTooltip(pathway)
-        })
-    END FOR
-    plot.colorScale ← {
-        label: "-log10(FDR)",
-        scheme: "viridis",
-        min: 0,
-        max: MAX(-LOG10(p.padjusted) for p in topPathways)
-    }
-    plot.sizeScale ← {
-        label: "Gene Count",
-        min: 5,
-        max: 20
-    }
-    RETURN plot
-END
-SUBROUTINE: GeneratePCAPlot
-INPUT: expressionData, metadata, title
-OUTPUT: plot (Plot object)
-BEGIN
-    // Perform PCA on normalized expression data
-    // Transpose so samples are rows
-    dataMatrix ← TRANSPOSE(expressionData)
-    // Center and scale data
-    centeredData ← CenterAndScale(dataMatrix)
-    // Compute principal components
-    pcaResult ← ComputePCA(centeredData, numComponents = 3)
-    plot ← {
-        type: "scatter",
-        title: title,
-        xLabel: "PC1 ({pcaResult.explainedVariance[0]}%)",
-        yLabel: "PC2 ({pcaResult.explainedVariance[1]}%)",
-        points: []
-    }
-    // Plot samples
-    FOR i ← 0 TO length(metadata.samples) - 1 DO
-        sample ← metadata.samples[i]
-        plot.points.append({
-            x: pcaResult.components[i][0],
-            y: pcaResult.components[i][1],
-            color: metadata.groups[i],
-            shape: metadata.replicates[i],
-            size: 10,
-            label: sample,
-            tooltip: FormatSampleTooltip(sample, metadata)
-        })
-    END FOR
-    plot.legend ← {
-        colorBy: "Treatment Group",
-        shapeBy: "Replicate"
-    }
-    RETURN plot
-END
-```
-**Complexity Analysis**:
-- **Time**: O(G × S + G log G) for heatmap with clustering
-- **Space**: O(G × S) for expression matrix
-- **Typical Performance**: 5-30 seconds depending on plot complexity
----
-## Algorithm 3: HTML Report Generation
-**Purpose**: Create interactive HTML report with embedded visualizations.
-```
-ALGORITHM: GenerateHTMLReport
-INPUT: reportData, visualizations, config
-OUTPUT: htmlReport (string)
-BEGIN
-    html ← []
-    // === Header Section ===
-    html.append("""
-    <!DOCTYPE html>
-    <html lang="en">
-    <head>
-        <meta charset="UTF-8">
-        <title>CRISPR-Cas13 Analysis Report</title>
-        <style>
-            {CSS_STYLES}
-        </style>
-        <script src="https://cdn.plot.ly/plotly-2.26.0.min.js"></script>
-        <script src="https://code.jquery.com/jquery-3.7.0.min.js"></script>
-    </head>
-    <body>
-    """)
-    // === Title and Summary ===
-    html.append("""
-    <div class="header">
-        <h1>CRISPR-Cas13 Bioinformatics Analysis Report</h1>
-        <p class="metadata">
-            <strong>Project:</strong> {reportData.metadata.projectName}<br>
-            <strong>Analysis Date:</strong> {reportData.metadata.analysisDate}<br>
-            <strong>Pipeline Version:</strong> {reportData.metadata.pipelineVersion}<br>
-            <strong>Reference Genome:</strong> {reportData.metadata.referenceGenome}
-        </p>
-    </div>
-    """)
-    // === Executive Summary ===
-    html.append(GenerateExecutiveSummary(reportData))
-    // === Table of Contents ===
-    html.append("""
-    <nav class="toc">
-        <h2>Table of Contents</h2>
-        <ul>
-            <li><a href="#alignment">1. Read Alignment Analysis</a></li>
-            <li><a href="#offtarget">2. Off-Target Prediction</a></li>
-            <li><a href="#expression">3. Differential Expression Analysis</a></li>
-            <li><a href="#pathways">4. Immune Pathway Enrichment</a></li>
-            <li><a href="#quality">5. Quality Metrics</a></li>
-            <li><a href="#methods">6. Methods</a></li>
-        </ul>
-    </nav>
-    """)
-    // === Section 1: Alignment ===
-    html.append(GenerateAlignmentSection(reportData.alignment, visualizations))
-    // === Section 2: Off-Target ===
-    IF reportData.offTarget != null THEN
-        html.append(GenerateOffTargetSection(reportData.offTarget, visualizations))
-    END IF
-    // === Section 3: Expression ===
-    IF reportData.expression != null THEN
-        html.append(GenerateExpressionSection(reportData.expression, visualizations))
-    END IF
-    // === Section 4: Pathways ===
-    IF reportData.expression != null THEN
-        html.append(GeneratePathwaySection(reportData.expression.enrichedPathways, visualizations))
-    END IF
-    // === Section 5: Quality Metrics ===
-    html.append(GenerateQualitySection(reportData.qualityMetrics, visualizations))
-    // === Section 6: Methods ===
-    html.append(GenerateMethodsSection(config))
-    // === Footer ===
-    html.append("""
-    <footer>
-        <p>Generated by CRISPR-Cas13 Bioinformatics Pipeline v{config.version}</p>
-        <p>Processing Time: {reportData.processingStats.totalTime} seconds</p>
-    </footer>
-    </body>
-    </html>
-    """)
-    htmlReport ← JOIN(html, "\n")
-    RETURN htmlReport
-END
-SUBROUTINE: GenerateExecutiveSummary
-INPUT: reportData
-OUTPUT: htmlSection (string)
-BEGIN
-    section ← []
-    section.append("""
-    <section class="executive-summary">
-        <h2>Executive Summary</h2>
-        <div class="summary-grid">
-    """)
-    // Alignment metrics card
-    section.append("""
-    <div class="metric-card">
-        <h3>Read Alignment</h3>
-        <div class="metric-value">{reportData.alignment.alignmentRate}%</div>
-        <div class="metric-label">Alignment Rate</div>
-        <p>{FormatNumber(reportData.alignment.alignedReads)} / {FormatNumber(reportData.alignment.totalReads)} reads aligned</p>
-    </div>
-    """)
-    // Off-target metrics card
-    IF reportData.offTarget != null THEN
-        section.append("""
-        <div class="metric-card {GetRiskClass(reportData.offTarget)}">
-            <h3>Off-Target Prediction</h3>
-            <div class="metric-value">{reportData.offTarget.highConfidenceOffTargets}</div>
-            <div class="metric-label">High-Confidence Off-Targets</div>
-            <p>{reportData.offTarget.totalGRNAs} gRNAs analyzed</p>
-        </div>
-        """)
-    END IF
-    // Expression metrics card
-    IF reportData.expression != null THEN
-        section.append("""
-        <div class="metric-card">
-            <h3>Differential Expression</h3>
-            <div class="metric-value">{reportData.expression.significantDEGs}</div>
-            <div class="metric-label">Significant DEGs</div>
-            <p>{reportData.expression.upregulatedGenes} up, {reportData.expression.downregulatedGenes} down</p>
-        </div>
-        """)
-    END IF
-    // Immune score card
-    IF reportData.expression != null THEN
-        immuneScoreClass ← GetImmuneScoreClass(reportData.expression.immuneScore)
-        section.append("""
-        <div class="metric-card {immuneScoreClass}">
-            <h3>Immune Activation</h3>
-            <div class="metric-value">{reportData.expression.immuneScore}/100</div>
-            <div class="metric-label">Immune Score</div>
-            <p>{GetImmuneScoreInterpretation(reportData.expression.immuneScore)}</p>
-        </div>
-        """)
-    END IF
-    section.append("""
-        </div>
-    </section>
-    """)
-    RETURN JOIN(section, "\n")
-END
-SUBROUTINE: GenerateAlignmentSection
-INPUT: alignmentData, visualizations
-OUTPUT: htmlSection (string)
-BEGIN
-    section ← []
-    section.append("""
-    <section id="alignment">
-        <h2>1. Read Alignment Analysis</h2>
-        <div class="subsection">
-            <h3>1.1 Alignment Statistics</h3>
-            <table class="data-table">
-                <tr>
-                    <th>Metric</th>
-                    <th>Value</th>
-                </tr>
-                <tr>
-                    <td>Total Reads</td>
-                    <td>{FormatNumber(alignmentData.totalReads)}</td>
-                </tr>
-                <tr>
-                    <td>Aligned Reads</td>
-                    <td>{FormatNumber(alignmentData.alignedReads)} ({alignmentData.alignmentRate}%)</td>
-                </tr>
-                <tr>
-                    <td>Unmapped Reads</td>
-                    <td>{FormatNumber(alignmentData.unmappedReads)}</td>
-                </tr>
-                <tr>
-                    <td>Multi-mapped Reads</td>
-                    <td>{FormatNumber(alignmentData.multiMappedReads)}</td>
-                </tr>
-                <tr>
-                    <td>Average MAPQ</td>
-                    <td>{alignmentData.averageMAPQ}</td>
-                </tr>
-            </table>
-        </div>
-        <div class="subsection">
-            <h3>1.2 Coverage Statistics</h3>
-            <table class="data-table">
-                <tr>
-                    <th>Metric</th>
-                    <th>Value</th>
-                </tr>
-                <tr>
-                    <td>Mean Coverage</td>
-                    <td>{alignmentData.coverageStatistics.meanCoverage}×</td>
-                </tr>
-                <tr>
-                    <td>Median Coverage</td>
-                    <td>{alignmentData.coverageStatistics.medianCoverage}×</td>
-                </tr>
-                <tr>
-                    <td>Coverage ≥10×</td>
-                    <td>{alignmentData.coverageStatistics.coverage10x}%</td>
-                </tr>
-                <tr>
-                    <td>Coverage ≥30×</td>
-                    <td>{alignmentData.coverageStatistics.coverage30x}%</td>
-                </tr>
-                <tr>
-                    <td>Uniformity</td>
-                    <td>{alignmentData.coverageStatistics.uniformity}</td>
-                </tr>
-            </table>
-        </div>
-        <div class="subsection">
-            <h3>1.3 Visualizations</h3>
-            {EmbedVisualization(visualizations, "alignment_pie")}
-            {EmbedVisualization(visualizations, "coverage_histogram")}
-        </div>
-    </section>
-    """)
-    RETURN JOIN(section, "\n")
-END
-SUBROUTINE: EmbedVisualization
-INPUT: visualizations, plotId
-OUTPUT: htmlDiv (string)
-BEGIN
-    plot ← FindPlotById(visualizations, plotId)
-    IF plot == null THEN
-        RETURN "<p>Visualization not available</p>"
-    END IF
-    // Convert plot to Plotly JSON
-    plotlyJson ← ConvertToPlotlyFormat(plot)
-    htmlDiv ← """
-    <div class="plot-container" id="{plotId}">
-        <script>
-            Plotly.newPlot('{plotId}', {plotlyJson.data}, {plotlyJson.layout}, {plotlyJson.config});
-        </script>
-    </div>
-    """
-    RETURN htmlDiv
-END
-```
-**Complexity Analysis**:
-- **Time**: O(S × P) where S = sections, P = plots
-- **Space**: O(H) where H = HTML size (typically 1-10 MB)
-- **Generation Time**: 1-5 seconds
----
-## Algorithm 4: PDF Export
-**Purpose**: Generate print-friendly PDF report.
-```
-ALGORITHM: GeneratePDFReport
-INPUT: htmlReport (string), outputPath (string)
-OUTPUT: pdfFile (path)
-BEGIN
-    // Use headless browser for HTML→PDF conversion
-    // Supports WeasyPrint, Puppeteer, or similar
-    TRY
-        // Option 1: WeasyPrint (Python)
-        IF HasWeasyPrint() THEN
-            pdf ← WeasyPrint.HTML(htmlReport).write_pdf(outputPath)
-        // Option 2: Puppeteer (Node.js)
-        ELSE IF HasPuppeteer() THEN
-            browser ← LaunchBrowser(headless = true)
-            page ← browser.newPage()
-            page.setContent(htmlReport)
-            page.pdf({
-                path: outputPath,
-                format: 'A4',
-                printBackground: true,
-                margin: {top: '1cm', right: '1cm', bottom: '1cm', left: '1cm'}
-            })
-            browser.close()
-        ELSE
-            RETURN error("No PDF renderer available")
-        END IF
-        LogInfo("PDF report generated: {outputPath}")
-        RETURN outputPath
-    CATCH RenderError AS e DO
-        LogError("PDF generation failed: {e.message}")
-        RETURN null
-    END TRY
-END
-```
-**Complexity Analysis**:
-- **Time**: O(P) where P = page count (typically 5-30 seconds)
-- **Space**: O(H) for HTML rendering
-- **File Size**: 2-20 MB depending on plot complexity
----
-## Algorithm 5: Data Export (VCF, BED, CSV)
-**Purpose**: Export analysis results in standard bioinformatics formats.
-```
-ALGORITHM: ExportAnalysisResults
-INPUT: reportData, outputDirectory, config
-OUTPUT: exportedFiles (array of paths)
-BEGIN
-    exportedFiles ← []
-    // === Export 1: VCF (Variant Call Format) for off-targets ===
-    IF reportData.offTarget != null THEN
-        vcfPath ← outputDirectory + "/offtargets.vcf"
-        vcfFile ← OpenFile(vcfPath, mode = "write")
-        // Write VCF header
-        vcfFile.WriteLine("##fileformat=VCFv4.2")
-        vcfFile.WriteLine("##fileDate={FormatDate(GetCurrentTime())}")
-        vcfFile.WriteLine("##source=CRISPR-Cas13-Pipeline-v{config.version}")
-        vcfFile.WriteLine("##reference={config.referenceGenome}")
-        vcfFile.WriteLine("##INFO=<ID=GRNA,Number=1,Type=String,Description=\"Guide RNA sequence\">")
-        vcfFile.WriteLine("##INFO=<ID=OTS,Number=1,Type=Float,Description=\"Off-target score\">")
-        vcfFile.WriteLine("##INFO=<ID=MM,Number=1,Type=Integer,Description=\"Number of mismatches\">")
-        vcfFile.WriteLine("#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO")
-        // Write off-target sites
-        FOR EACH gRNA IN reportData.offTarget.gRNAs DO
-            FOR EACH site IN gRNA.offTargetSites DO
-                chrom ← site.chromosome
-                pos ← site.position
-                id ← site.id
-                ref ← site.referenceAllele
-                alt ← site.alternateAllele
-                qual ← ROUND(site.offTargetScore × 100)
-                filter ← IF site.offTargetScore >= 0.7 THEN "PASS" ELSE "LowScore"
-                info ← "GRNA={gRNA.sequence};OTS={site.offTargetScore};MM={site.mismatches}"
-                vcfFile.WriteLine("{chrom}\t{pos}\t{id}\t{ref}\t{alt}\t{qual}\t{filter}\t{info}")
-            END FOR
-        END FOR
-        vcfFile.Close()
-        exportedFiles.append(vcfPath)
-        LogInfo("Exported VCF: {vcfPath}")
-    END IF
-    // === Export 2: BED (Browser Extensible Data) for genome browser ===
-    bedPath ← outputDirectory + "/coverage.bed"
-    bedFile ← OpenFile(bedPath, mode = "write")
-    bedFile.WriteLine("track name=\"CRISPR_Coverage\" description=\"RNA-seq coverage\" visibility=2 color=0,0,255")
-    FOR EACH region IN reportData.alignment.coverageRegions DO
-        bedFile.WriteLine("{region.chrom}\t{region.start}\t{region.end}\t{region.name}\t{region.score}\t{region.strand}")
-    END FOR
-    bedFile.Close()
-    exportedFiles.append(bedPath)
-    LogInfo("Exported BED: {bedPath}")
-    // === Export 3: CSV for differential expression ===
-    IF reportData.expression != null THEN
-        csvPath ← outputDirectory + "/differential_expression.csv"
-        csvFile ← OpenFile(csvPath, mode = "write")
-        // Write header
-        csvFile.WriteLine("GeneID,GeneSymbol,BaseMean,Log2FoldChange,PValue,AdjustedPValue,Biotype")
-        // Write gene results
-        FOR EACH gene IN reportData.expression.allGenes DO
-            csvFile.WriteLine(
-                "{gene.geneId}," +
-                "{gene.geneSymbol}," +
-                "{gene.baseMean}," +
-                "{gene.log2FoldChange}," +
-                "{gene.pvalue}," +
-                "{gene.padj}," +
-                "{gene.biotype}"
-            )
-        END FOR
-        csvFile.Close()
-        exportedFiles.append(csvPath)
-        LogInfo("Exported CSV: {csvPath}")
-    END IF
-    // === Export 4: JSON for programmatic access ===
-    jsonPath ← outputDirectory + "/report_data.json"
-    WriteJSON(reportData, jsonPath, indent = 2)
-    exportedFiles.append(jsonPath)
-    LogInfo("Exported JSON: {jsonPath}")
-    RETURN exportedFiles
-END
-```
-**Complexity Analysis**:
-- **Time**: O(N) where N = total data points
-- **Space**: O(N) for file buffers
-- **Export Time**: 1-10 seconds depending on data size
----
-## Algorithm 6: Main Reporting Pipeline
-**Purpose**: Orchestrate complete reporting workflow.
-```
-ALGORITHM: GenerateComprehensiveReport
-INPUT: alignmentResults, offTargetResults, expressionResults, config
-OUTPUT: reportBundle (ReportBundle object)
-BEGIN
-    startTime ← GetCurrentTime()
-    LogInfo("Starting comprehensive report generation...")
-    // Step 1: Aggregate data
-    LogInfo("Aggregating report data...")
-    reportData ← AggregateReportData(
-        alignmentResults,
-        offTargetResults,
-        expressionResults,
-        config
-    )
-    // Step 2: Generate visualizations
-    LogInfo("Generating visualizations...")
-    visualizations ← GenerateVisualizations(reportData, config.visualization)
-    // Step 3: Generate HTML report
-    LogInfo("Generating HTML report...")
-    htmlReport ← GenerateHTMLReport(reportData, visualizations, config)
-    htmlPath ← config.outputDirectory + "/report.html"
-    WriteFile(htmlPath, htmlReport)
-    // Step 4: Generate PDF (optional)
-    pdfPath ← null
-    IF config.generatePDF THEN
-        LogInfo("Generating PDF report...")
-        pdfPath ← GeneratePDFReport(htmlReport, config.outputDirectory + "/report.pdf")
-    END IF
-    // Step 5: Export data files
-    LogInfo("Exporting analysis results...")
-    exportedFiles ← ExportAnalysisResults(reportData, config.outputDirectory, config)
-    // Step 6: Generate summary statistics file
-    summaryPath ← config.outputDirectory + "/summary.txt"
-    WriteSummaryFile(reportData, summaryPath)
-    exportedFiles.append(summaryPath)
-    processingTime ← GetCurrentTime() - startTime
-    reportBundle ← {
-        htmlReport: htmlPath,
-        pdfReport: pdfPath,
-        exportedFiles: exportedFiles,
-        visualizations: visualizations,
-        reportData: reportData,
-        generationTime: processingTime,
-        timestamp: GetCurrentTime()
-    }
-    LogInfo("Report generation complete in {processingTime}s")
-    LogInfo("HTML report: {htmlPath}")
-    IF pdfPath != null THEN
-        LogInfo("PDF report: {pdfPath}")
-    END IF
-    RETURN reportBundle
-END
-SUBROUTINE: WriteSummaryFile
-INPUT: reportData, outputPath
-OUTPUT: none
-BEGIN
-    file ← OpenFile(outputPath, mode = "write")
-    file.WriteLine("=" × 80)
-    file.WriteLine("CRISPR-Cas13 Analysis Summary")
-    file.WriteLine("=" × 80)
-    file.WriteLine("")
-    file.WriteLine("Project: {reportData.metadata.projectName}")
-    file.WriteLine("Analysis Date: {reportData.metadata.analysisDate}")
-    file.WriteLine("Pipeline Version: {reportData.metadata.pipelineVersion}")
-    file.WriteLine("")
-    file.WriteLine("-" × 80)
-    file.WriteLine("READ ALIGNMENT")
-    file.WriteLine("-" × 80)
-    file.WriteLine("Total Reads: {FormatNumber(reportData.alignment.totalReads)}")
-    file.WriteLine("Aligned Reads: {FormatNumber(reportData.alignment.alignedReads)} ({reportData.alignment.alignmentRate}%)")
-    file.WriteLine("Mean Coverage: {reportData.alignment.coverageStatistics.meanCoverage}×")
-    file.WriteLine("")
-    IF reportData.offTarget != null THEN
-        file.WriteLine("-" × 80)
-        file.WriteLine("OFF-TARGET PREDICTION")
-        file.WriteLine("-" × 80)
-        file.WriteLine("gRNAs Analyzed: {reportData.offTarget.totalGRNAs}")
-        file.WriteLine("High-Confidence Off-Targets: {reportData.offTarget.highConfidenceOffTargets}")
-        file.WriteLine("")
-    END IF
-    IF reportData.expression != null THEN
-        file.WriteLine("-" × 80)
-        file.WriteLine("DIFFERENTIAL EXPRESSION")
-        file.WriteLine("-" × 80)
-        file.WriteLine("Genes Tested: {FormatNumber(reportData.expression.totalGenesTested)}")
-        file.WriteLine("Significant DEGs: {reportData.expression.significantDEGs}")
-        file.WriteLine("Upregulated: {reportData.expression.upregulatedGenes}")
-        file.WriteLine("Downregulated: {reportData.expression.downregulatedGenes}")
-        file.WriteLine("Immune Score: {reportData.expression.immuneScore}/100")
-        file.WriteLine("")
-    END IF
-    file.WriteLine("=" × 80)
-    file.Close()
-END
-```
-**Complexity Analysis**:
-- **Time**: O(G × S + P) where P = plot rendering time
-- **Space**: O(G × S + H) where H = HTML size
-- **End-to-End Performance**: 30 seconds to 5 minutes depending on dataset size
----
-## Error Handling
-### 1. Missing Data Handling
-```
-FUNCTION: HandleMissingData
-INPUT: reportData, requiredSections
-OUTPUT: modifiedReportData
-BEGIN
-    FOR EACH section IN requiredSections DO
-        IF reportData[section] == null THEN
-            LogWarning("Missing data for section: {section}")
-            reportData[section] ← CreatePlaceholderSection(section)
-        END IF
-    END FOR
-    RETURN reportData
-END
-```
-### 2. Visualization Failure Recovery
-```
-FUNCTION: GenerateVisualizationSafely
-INPUT: plotFunction, data, config
-OUTPUT: plot or placeholder
-BEGIN
-    TRY
-        plot ← plotFunction(data, config)
-        RETURN plot
-    CATCH VisualizationError AS e DO
-        LogError("Failed to generate plot: {e.message}")
-        RETURN CreatePlaceholderPlot(e.message)
-    END TRY
-END
-```
----
-## Performance Optimization
-### 1. Parallel Visualization Generation
-```
-FUNCTION: GenerateVisualizationsParallel
-INPUT: reportData, config, numThreads
-OUTPUT: visualizations
-BEGIN
-    plotTasks ← [
-        TASK(GenerateVolcanoPlot, reportData.expression),
-        TASK(GenerateHeatmap, reportData.expression),
-        TASK(GeneratePathwayDotPlot, reportData.expression),
-        // ... more plot tasks
-    ]
-    visualizations ← ParallelExecute(plotTasks, numThreads = numThreads)
-    RETURN visualizations
-END
-```
----
-## References
-1. Hunter, J. D. (2007). Matplotlib: A 2D graphics environment. *Computing in Science & Engineering*.
-2. Plotly Technologies Inc. (2015). Collaborative data science. https://plot.ly
-3. IGV: Integrative Genomics Viewer. https://software.broadinstitute.org/software/igv/
----
-**End of Pseudocode Documentation**