Properties

_images/properties_dialog.png

EnrichmentMap has some semi-hidden properties than can be used to customize the behavior of the App.

To manually edit these properties go to the Cytoscape main menu and select Edit > Preferences > Properties…. Then select org.baderlab.enrichmentmap in the Cytoscape Preferences Editor.

Supported properties:

heatmapAutofocus
  • If true then selecting a node/edge in the network will automatically bring the Heat Map panel to the front.
  • This property can also be changed from the Heat Map using the Panel Menu.
  • Default Value: false
  • Allowed Values: true, false
  • img1
default.distanceMetric
  • Specifies the how the Hierarchical Clustering algorithm calculates distance.
  • This property can also be changed from the Heat Map using the Panel Menu.
  • Default Value: PEARSON
  • Allowed Values: PEARSON, EUCLIDEAN, COSINE
  • img2
create.warn
  • When creating a network with the Create EnrichmentMap Dialog sometimes a validation warning dialog will be shown if there are any issues that need to be brought to the user’s attention. If this property is set to false then the warning dialog will never be shown even if there are issues. Note: The dialog will still be shown if there are errors that prevent the network from being created.
  • Default Value: true
  • Allowed Values: true, false
  • img3
default.pvalue
  • Default p-value in the Create EnrichmentMap Dialog
  • Default Value: 1.0
  • Allowed Values: > 0.0, < 1.0
  • img4
default.qvalue
  • Default q-value in the Create EnrichmentMap Dialog
  • Default Value: 0.1
  • Allowed Values: > 0.0, < 1.0
  • img5