Difference between revisions of "Add expression values (analysis)"

Latest revision as of 16:33, 12 March 2019

Analysis title

Add expression values

Provider

Institute of Systems Biology

Class

ExpressionFilterAnalysis

Plugin

biouml.plugins.expression (Expression display for diagrams)

[edit] Description

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

[edit] 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
    • Color for not presented – Color to represent missed value (when row exists in the table, but value is not a number or empty).
    • Gradient fill – Use fading gradient aura
  • 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
    • Color for not presented – Color to represent missed value (when row exists in the table, but value is not a number or empty).
  • 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