PathLay
  • Welcome to PathLay’s documentation!
  • Features
  • Requirements
    • For Building the Docker Image (Recommended)
    • For the Apache Server Installation
  • Installation
    • Installation on Linux
      • Installation using Docker (Recommended)
      • Installation with .deb package
      • Apache Server Installation
  • How to run
    • Run PathLay as network server with Docker
    • Run PathLay as local server with Docker (localhost)
  • Usage
    • Account Managing
      • Register a New Account
      • Login to an Existing Account
    • Experiment Package
      • Configuration File
      • Datasets Files
      • Supported IDs
    • Database Configuration
      • Organism Selection
      • Interaction Files
      • Pathway Files
      • Alternative installation
    • Home Manager
      • Creating an Experiment Package
        • Adding a new Experiment Package
        • Uploading a new Experiment Package
      • Editing an Experiment Package
        • Edit Experiment’s General Information
        • Configure a Dataset
        • Gene Ontologies
      • Downloading an Experiment Package
    • Configuration Page
      • Maps Databases
      • Data Selection
      • Configuring Filters for a Dataset
        • Filtering Options
        • ID Preservation
        • Transcription Factors
          • Transcription Factors ID Preservation
        • Non Differentially Expressed IDs
          • Loading Non Differentially Expressed IDs from TFs
      • Maps Restriction Procedure
        • Pooling
        • Intersect
    • Pathway Explorer
      • Pathway Navigation
      • Main Menu
      • Highlighting Feature
      • The Clipboard
      • The Selectors Section
        • Select by IDs
        • Select by Agreement
      • Settings
        • Transparency and Size
        • Screenshot
    • Indicators
      • Legend and Explanation
      • Drawing Rationale
        • Gene/Protein Circuit
          • Single Gene/Protein
          • Multiple Genes/Proteins Circuit
        • miRNAs Circuit
        • Transcription Factors Circuit
        • Methylation Circuit
        • Chromatin Status Circuit
  • License
  • Support
  • Contribute
PathLay
  • Usage
  • Pathway Explorer
  • Main Menu
  • View page source

Main Menu

The “PathLay - MAPS” page provides different features in six sections accessible from a menu located in the upper right corner of the page:

  • Highlight: Provides the selectors to highlight indicators containing specific components

  • Screenshot: Creates a downloadable image of a map with its indicators

  • Clipboard: Open or close Clipboard

  • Settings: Allows tuning of indicators transparency and size

  • Selectors: Provides the main query system for pathway and indicator filtering

  • ?: Displays helpful information regarding the interpratation of the indicators

These sections and the respective features will be explained in detail later.

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© Copyright 2022, Matteo Ramazzotti Lorenzo Casbarra.

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