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deepTools PlotHeatmap Specifications

Process Details

  • Name: deepTools_PlotHeatmap
  • Process UUID: 7c306afdb6e54924b5d6dd6440055cdb
  • Process Group: Misc.

Overview

deepTools PlotHeatmap is a visualization tool from deepTools version 3.5.6 that generates heatmaps from bigwig files. This process creates a heatmap visualization of peaks matrices, allowing researchers to visualize genomic signal patterns across regions of interest in a comprehensive and customizable format.

This process is implemented in Bash, which invokes deepTools' plotHeatmap command for generating genomic heatmap visualizations.

Key Functionality

  • Matrix Visualization: Converts compressed matrix files into publication-ready heatmaps
  • Customizable Sorting: Provides multiple options for organizing regions in the heatmap display
  • Flexible Output Formats: Supports multiple image formats including PNG, PDF, SVG, and EPS
  • Publication-Ready Graphics: Offers extensive customization options for plot appearance and dimensions

Input/Output Specification

Inputs

Required Inputs

  • Zipped Matrix File
    • Description: Compressed matrix file containing genomic signal data for heatmap generation
    • Format: GZ (gzip compressed file)

Outputs

  • Heatmap Image
    • Description: Generated heatmap visualization of the genomic data matrix
    • Format: PNG (or user-specified format)

Parameters & Settings

These parameters can be adjusted in the Foundry UI when running this process.

  • Plot Title

    • Description: Title of the plot, to be printed on top of the generated image. Leave blank for no title.
    • Default value: (blank)

  • Sort Regions

    • Description: Whether the heatmap should present the regions sorted. The default is to sort in descending order based on the mean value per region. Note that 'keep' and 'no' are the same thing.
    • Available options: descend (default), ascend, no, keep

  • Alpha

    • Description: The alpha channel (transparency) to use for the heatmaps. The default is 1.0 and values must be between 0 and 1.
    • Default value: 1

  • Heatmap Width

    • Description: Width of the heatmap in centimeters
    • Default value: 20

  • Heatmap Height

    • Description: Plot height in cm. The default for the heatmap height is 28. The minimum value is 3 and the maximum is 100.
    • Default value: 28

  • Plot DPI

    • Description: Set the DPI to save the figure.
    • Default value: 200

  • Plot Type

    • Description: 'lines' will plot the profile line based on the average type selected. 'fill' fills the region between zero and the profile curve. The fill in color is semitransparent to distinguish different profiles. 'se' and 'std' color the region between the profile and the standard error or standard deviation of the data.
    • Available options: lines (default), fill, se, std

  • Plot File Format

    • Description: Image format type. If given, this option overrides the image format based on the plotFile ending. The available options are: 'png', 'eps', 'pdf', 'plotly' and 'svg'
    • Available options: png (default), eps, pdf, plotly, svg

References & Resources

  • Tool Documentation: Contact the team for details on plotHeatmap
  • Related Papers: Ramírez, F., Ryan, D. P., Grüning, B., Bhardwaj, V., Kilpert, F., Richter, A. S., ... & Manke, T. (2016). deepTools2: a next generation web server for deep-sequencing data analysis. Nucleic acids research, 44(W1), W160-W165.