Add expression values (analysis)

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Analysis title
Molecular-networks-Add-expression-values-icon.png Add expression values
Provider
Institute of Systems Biology
Class
ExpressionFilterAnalysis
Plugin
biouml.plugins.expression (Expression display for diagrams)

Description

This analysis allows you to display expression values as molecules background on the specified diagram.

Parameters:

  • Input diagram – Input diagram
  • Mapping properties – Mapping properties
    • Table – Table to use expression values from
    • Use outside fill – When checked, outside fill will be used
    • Outside filling options – Outside filling options
      • Columns – List of columns to create outside fill
      • Width of the fill – Range from 1 to 40
      • Minimum value – Lowest value in the selected columns
      • Start-color – Color for minimum value
      • Maximum value – Highest value in the selected columns
      • End-color – Color for maximum value
      • Use color for zero – If checked, zero-color will be used to represent zero value
      • Zero color – Color to represent zero value. Used only if minimum value 0, maximum value > 0 and 'Use color for zero' is checked.
      • Zero level – Value at which zero color will be used
    • Use inside fill – When checked, inside fill will be used
    • Inside filling options – Inside filling options
      • Column – Column to create inside fill
      • Minimum value – Lowest value in the selected columns
      • Start-color – Color for minimum value
      • Maximum value – Highest value in the selected columns
      • End-color – Color for maximum value
      • Use color for zero – If checked, zero-color will be used to represent zero value
      • Zero color – Color to represent zero value. Used only if minimum value 0, maximum value > 0 and 'Use color for zero' is checked.
      • Zero level – Value at which zero color will be used
    • Use p-value stars – When checked, a number of stars will be added to matched elements depending on p-value
    • P-value stars options – *** options
      • Column – Column with p-values
      • * cutoff – If value below this cutoff, one star is displayed
      • ** cutoff – If value below this cutoff, two stars are displayed
      • *** cutoff – If value below this cutoff, three stars are displayed
    • Use flux edges – When checked, a reaction edges thickness will be changed based on reaction speed data
    • Flux options – Flux options
      • Column – Column to create inside fill
      • Minimum value – Lowest value in the selected columns
      • Maximum value – Highest value in the selected columns
      • Maximum stroke width – Maximum stroke width
  • Output diagram – Output diagram
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