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Welcome to PyIOmica’s documentation!

This documentation describes PyIOmica, a Python package that provides bioinformatics utilities for analyzing (dynamic) omics datasets. PyIOmica extends MathIOmica usage to Python and implements new visualizations and computational tools for graph analyses.

Contents:

• 1. Overview
  • Versions
  • Documentation
  • Additional information
  • Licensing
  • Contact information
  • Funding
• 2. Installation
  • Pre-Installation Requirements
  • Installation Instructions
  • Running PyIOmica
• 3. Functionality
  • Global variables
    • printPackageGlobalDefaults
    • PackageDirectory
    • ConstantPyIOmicaDataDirectory
    • ConstantPyIOmicaExamplesDirectory
    • ConstantPyIOmicaExampleVideosDirectory
    • ConstantGeneDictionary
  • Categorization functions
    • calculateTimeSeriesCategorization()
    • clusterTimeSeriesCategorization()
    • visualizeTimeSeriesCategorization()
  • Enrichment analyses functions
    • internalAnalysisFunction()
    • OBOGODictionary()
    • GetGeneDictionary()
    • GOAnalysisAssigner()
    • obtainConstantGeneDictionary()
    • GOAnalysis()
    • GeneTranslation()
    • KEGGAnalysisAssigner()
    • KEGGDictionary()
    • KEGGAnalysis()
    • MassMatcher()
    • MassDictionary()
    • ExportEnrichmentReport()
    • BenjaminiHochbergFDR()
    • ReactomeAnalysis()
    • ExportReactomeEnrichmentReport()
  • Extended DataFrame and data-processing functions
    • DataFrame
      • DataFrame.__init__()
      • DataFrame.filterOutAllZeroSignals()
      • DataFrame.filterOutFractionZeroSignals()
      • DataFrame.filterOutFractionMissingSignals()
      • DataFrame.filterOutReferencePointZeroSignals()
      • DataFrame.tagValueAsMissing()
      • DataFrame.tagMissingAsValue()
      • DataFrame.tagLowValues()
      • DataFrame.removeConstantSignals()
      • DataFrame.boxCoxTransform()
      • DataFrame.modifiedZScore()
      • DataFrame.normalizeSignalsToUnity()
      • DataFrame.quantileNormalize()
      • DataFrame.compareTimeSeriesToPoint()
      • DataFrame.compareTwoTimeSeries()
      • DataFrame.imputeMissingWithMedian()
    • mergeDataframes()
    • getLombScarglePeriodogramOfDataframe()
    • getRandomSpikesCutoffs()
    • getRandomAutocorrelations()
    • getRandomPeriodograms()
  • Clustering functions
    • getEstimatedNumberOfClusters()
    • getNClustersFromLinkageElbow()
    • getNClustersFromLinkageSilhouette()
    • runForClusterNum()
    • getGroupingIndex()
    • makeClusteringObject()
    • exportClusteringObject()
    • getCommunitiesOfTimeSeries()
  • Frequency Based Subject Match
    • bootstrapGeneral()
    • calculateLinksBetweenSubjectsByDistance()
    • calculateLinksBetweenSubjectsByCorrelation()
    • getCommunityStructure()
    • getCommunityGenesDict()
    • splitGenes()
    • getCommunityTopGenesByNumber()
    • getCommunityTopGenesByFrequencyRanking()
    • optimizeK()
  • Visibility graph preparation functions
    • getAdjacencyMatrixOfNVG()
    • getAdjacencyMatrixOfNVGbyNUMPY()
    • getAdjacencyMatrixOfHVG()
    • getAdjacencyMatrixOfHVGbyNUMPY()
  • Visibility Graph Community Detection
    • createVisibilityGraph()
    • communityDetectByPathLength()
  • Visualization functions
    • saveFigure()
    • makeDataHistograms()
    • makeLombScarglePeriodograms()
    • addVisibilityGraph()
    • makeVisibilityGraph()
    • makeVisibilityBarGraph()
    • makePlotOfPeak()
    • addColorbarToFigure()
    • makeDendrogramHeatmapOfClusteringObject()
    • plotHVGBarGraphDual()
    • plotNVGBarGraphDual()
  • Utility functions
    • readMathIOmicaData()
    • runCPUs()
    • createReverseDictionary()
    • createDirectories()
  • Data Storage
    • read()
    • write()
• 4. Dependencies
• 5. Included data
• 6. Examples
  • Enrichment report
  • Import of MathIOmica Objects
  • Clustering object export example
  • GO Analysis examples
  • KEGG Analysis examples
  • Reactome Analysis examples
  • Visibility Graph examples
  • Visibility Graph Community Detection
  • Extended DataFrame
  • Time Series Categorization

Indices and tables

• Index

• Module Index

• Search Page