Screenshot of the complex Options Window.


The use and settings for complexes in the MST can be modified using this window. The window contains tabs for different groups of settings.

Complex

Example of a complex, highlighted by red background color. The complex label shows the name of the Complex, 'CC 1'.
  • Use Complexes: check to enable the usage of complexes. Complexes are groups of related isolates. More precisely, complexes are groups of nodes in which every node has a certain maximum distance to at least one other member of the complex.
  • Use generated colors/Use color: Complexes are displayed by highlighting the background of the nodes in a complexes and their connection lines. The color of this highlights can generated automatically or a color can be set for all complexes.
  • Show Complex labels: Defined if the complex names should be shown as labels in the MST.
  • Name prefix: The name of a complex consists of this prefix (by default "Complex") followed by an incrementing number.
  • Maximum distance in Complex: The maximum distance two nodes can have if they are considered to be in the same complex.
  • Minimum number of Samples/Nodes: The minimum number of Samples or MST Nodes (specified below) that are required for a complex.
  • Use for minimum: Select if minimum calculation above should use Samples or MST Nodes.
  • Order Complexes by number of Samples or MST Nodes: The complex name consists of the defined prefix and a number. The numbering is either ordered descending by the number of Samples in a complex or by the number of MST Nodes.

Complex Label

The appearance of the labels for the complexes can be modified here.

  • Complex label font: Choose the font and size that is used to display the label.
  • Complex label color: Choose the color that is used to paint the Complex label.
  • Distance from label to founder: Defines how close a complex label is located to the founding node (default: 1).
  • Draw box around label: Check to draw a box around the complex label

The next three options define if a line should be drawn from the complex label to the founder. If line style is other than none, the line color and line width can be specified.