Network Visualization

Using a *.txt file storing symmetric connectivity matrix and a *.csv table with nodal information (such as coordinate, label, module and color) as input, we can draw spheres and rods to visualize nodes and edges.

  • surface: surface file
  • alpha: degree of opaque
  • display: mode of display
  • node: node file defined as csv table. All columns are optional except for ‘x’, ‘y’ and ‘z’.

For example:

 x     y    z  size  module   r   g   b   label
 -1 , 20 , 20 , 4 , module1 , 5 , 5 , 5 , node1
-10 , 22 , 20 , 4 , module1 , 5 , 5 , 5 , node2
 12 , 20 , 20 , 4 , module2 , 5 , 5 , 5 , node3
  • show node labels: check to show labels defined in input node file.
  • same size: use same size for all node, uncheck to use user defined size in input node file.
  • user defined node color: use color defined in input node file.
  • same node color: use same color for all node.
  • module color: use different color for each module. Modules are defined in input node file.
  • edge: edge matrix for input file, the number of rows and columns should be the same as input file.
  • display edges: display or not edges.
  • hide node without edge: select not to show nodes without edge
  • thickness: relative thickness for all edges
  • adjust edge color: use different color for positive and negative edge.
  • threshold: an expression that compatible with matlab syntax to filter out unwanted edges in edge matrix.
  • use summed weight as node radius: sum up node’s degree and define node size.
  • threshold: nodes with degree smaller than the threshold will not be shown.
  • Buttons:
    • S: Save parameters of the current panel to a *.mat file. The *.mat can be further loaded for the panel or be used in a script processing.
    • L: Load parameters from *.mat for the current panel.
    • ?: Help information.