Load an input network
With this menu, you can load networks in two formats currently not supported
by Cytoscape. Select the network file of your choice and click the GO button
in the main menu to load the network.
Network types
GDL networks
GDL networks can be generated by CoNet on command line.
They contain node and edge attributes and are the most convenient
way of loading a network computed with CoNet on command line into Cytoscape.
Adjacency matrices
Adjacency matrices are N x N matrices, where N is the number of rows in the
input matrix. A non-zero entry in an adjacency matrix represents an edge
(for instance, if A is an adjacency matrix and A(i,j)>0, then taxon i is connected to taxon j by an edge).
The value of the non-zero entry represents the score of the edge.
For instance, SparCC outputs an adjacency matrix with correlation scores
and a p-value matrix, both of which can be loaded via this menu.
Load
Select a GDL network or an adjacency matrix file by clicking on "Open file".
To undo a file selection, click "Open file" again and then "Cancel". This will clear the file selection.
If you want to load an adjacency matrix, you can optionally load a p-value matrix.
The p-value matrix is assumed to have the same order of rows and columns as the adjacency matrix.
Thus, the p-value matrix provides p-values for the edges stored in the adjacency matrix.
Adjacency matrix options
The scores in the adjacency matrix can be filtered using the lower and upper threshold text fields.
If no thresholds are provided, all edges coded by the adjacency matrix are read in.
The p-values in the p-value matrix can also be filtered by providing a threshold via the P-value
threshold field. If this field is left empty, edges with p-values above 0.05 are discarded.
Finally, p-values for adjacency matrices can be multiple-testing corrected, using Bonferroni
or Benjamini-Hochberg multiple testing correction.
If multiple-testing correction is applied, the p-value threshold refers to adjusted p-values.