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

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;Analysis title
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:[[File:Molecular-networks-Add-expression-values-icon.png]] Add expression values
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;Provider
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:[[Institute of Systems Biology]]
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;Class
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:{{Class|biouml.plugins.expression.ExpressionFilterAnalysis}}
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;Plugin
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:[[Biouml.plugins.expression (plugin)|biouml.plugins.expression (Expression display for diagrams)]]
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==== Description ====
 
This analysis allows you to display expression values as molecules background on the specified diagram.
 
This analysis allows you to display expression values as molecules background on the specified diagram.
  
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*** '''Zero color''' – Color to represent zero value. Used only if minimum value 0, maximum value > 0 and <nowiki>'</nowiki>Use color for zero<nowiki>'</nowiki> is checked.
 
*** '''Zero color''' – Color to represent zero value. Used only if minimum value 0, maximum value > 0 and <nowiki>'</nowiki>Use color for zero<nowiki>'</nowiki> is checked.
 
*** '''Zero level''' – Value at which zero color will be used
 
*** '''Zero level''' – Value at which zero color will be used
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*** '''Color for not presented''' – Color to represent missed value (when row exists in the table, but value is not a number or empty).
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*** '''Gradient fill''' – Use fading gradient aura
 
** '''Use inside fill''' – When checked, inside fill will be used
 
** '''Use inside fill''' – When checked, inside fill will be used
 
** '''Inside filling options''' – Inside filling options
 
** '''Inside filling options''' – Inside filling options
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*** '''Zero color''' – Color to represent zero value. Used only if minimum value 0, maximum value > 0 and <nowiki>'</nowiki>Use color for zero<nowiki>'</nowiki> is checked.
 
*** '''Zero color''' – Color to represent zero value. Used only if minimum value 0, maximum value > 0 and <nowiki>'</nowiki>Use color for zero<nowiki>'</nowiki> is checked.
 
*** '''Zero level''' – Value at which zero color will be used
 
*** '''Zero level''' – Value at which zero color will be used
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*** '''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
 
** '''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
 
** '''P-value stars options''' – *** options
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*** '''** cutoff''' – If value below this cutoff, two stars are displayed
 
*** '''** cutoff''' – If value below this cutoff, two stars are displayed
 
*** '''*** cutoff''' – If value below this cutoff, three stars are displayed
 
*** '''*** cutoff''' – If value below this cutoff, three stars are displayed
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** '''Use flux edges''' – When checked, a reaction edges thickness will be changed based on reaction speed data
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** '''Flux options''' – Flux options
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*** '''Column''' – Column to create inside fill
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*** '''Minimum value''' – Lowest value in the selected columns
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*** '''Maximum value''' – Highest value in the selected columns
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*** '''Maximum stroke width''' – Maximum stroke width
 
* '''Output diagram''' – Output diagram
 
* '''Output diagram''' – Output diagram
  
 
[[Category:Analyses]]
 
[[Category:Analyses]]
 
[[Category:Molecular networks (analyses group)]]
 
[[Category:Molecular networks (analyses group)]]
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[[Category:ISB analyses]]
 
[[Category:Autogenerated pages]]
 
[[Category:Autogenerated pages]]

Latest revision as of 16:33, 12 March 2019

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)

[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
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